diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 97c8c97f..237c9ed0 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,4 +1,5 @@ { + "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json", "name": "nfcore", "image": "nfcore/devcontainer:latest", diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index dd9ffa53..00000000 --- a/.editorconfig +++ /dev/null @@ -1,37 +0,0 @@ -root = true - -[*] -charset = utf-8 -end_of_line = lf -insert_final_newline = true -trim_trailing_whitespace = true -indent_size = 4 -indent_style = space - -[*.{md,yml,yaml,html,css,scss,js}] -indent_size = 2 - -# These files are edited and tested upstream in nf-core/modules -[/modules/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset -[/subworkflows/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset - -[/assets/email*] -indent_size = unset - -# ignore Readme -[README.md] -indent_style = unset - -# ignore python -[*.{py,md}] -indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 47f18382..00000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,118 +0,0 @@ -# `nf-cmgg/preprocessing`: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-cmgg/preprocessing. - -We try to manage the required tasks for nf-cmgg/preprocessing using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -## Contribution workflow - -If you'd like to write some code for nf-cmgg/preprocessing, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-cmgg/preprocessing issues](https://github.com/nf-cmgg/preprocessing/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-cmgg/preprocessing repository](https://github.com/nf-cmgg/preprocessing) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: - -```bash -nf-test test --profile debug,test,docker --verbose -``` - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- Open a pull-request from `patch` to `main`/`master` with the changes. - -## Pipeline contribution conventions - -To make the `nf-cmgg/preprocessing` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test in the `tests` directory. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. - -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-cmgg/preprocessing/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index d0f648f7..da749353 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,6 +9,7 @@ body: description: A clear and concise description of what the bug is. validations: required: true + - type: textarea id: command_used attributes: @@ -36,6 +37,6 @@ body: * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ * Version of nf-cmgg/preprocessing _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000..9ca8b695 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,7 @@ +contact_links: + - name: Join nf-core + url: https://nf-co.re/join + about: Please join the nf-core community here + - name: "Slack #preprocessing channel" + url: https://nfcore.slack.com/channels/preprocessing + about: Discussion about the nf-cmgg/preprocessing pipeline diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 8e00290d..451b7c69 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/preprocessing/tree/main/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/preprocessing/tree/master/docs/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/preprocessing/tree/main/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/preprocessing/tree/master/docs/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml index 34085279..e2833ee9 100644 --- a/.github/actions/get-shards/action.yml +++ b/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: ${{ env.NFT_VER }} - name: Get number of shards diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 9c844d5a..4175e3c8 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,24 +20,24 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: "${{ env.NFT_VER }}" install-pdiff: true - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@main + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0 - name: Set up Singularity if: contains(inputs.profile, 'singularity') @@ -46,6 +46,16 @@ runs: mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR + - name: Conda setup + if: contains(inputs.profile, 'conda') + uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 + with: + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge + channel-priority: strict + conda-remove-defaults: true + - name: Run nf-test shell: bash env: diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index b289ec4e..9c65e9a2 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -2,11 +2,13 @@ name: nf-core branch protection # This workflow is triggered on PRs to `main`/`master` branch on the repository # It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: - pull_request_target: + pull_request: branches: - main - master +permissions: {} + jobs: test: runs-on: ubuntu-latest @@ -14,33 +16,47 @@ jobs: # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'nf-cmgg/preprocessing' + env: + HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }} run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-cmgg/preprocessing ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ "$HEAD_REPO" == nf-cmgg/preprocessing ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - # If the above check failed, post a comment on the PR explaining the failure - # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - - name: Post PR comment + # If the above check failed, build a comment to be posted by the shared poster workflow + - name: Build PR comment if: failure() - uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 - with: - message: | - ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + BASE_REF: ${{ github.event.pull_request.base.ref }} + HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }} + PR_USER: ${{ github.event.pull_request.user.login }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "branch" > pr-comment/header.txt + cat > pr-comment/comment.md <> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + + download: + runs-on: ubuntu-latest + needs: configure + steps: + - name: Check out pipeline code + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + + - name: Install Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 + with: + python-version: "3.14" + architecture: "x64" + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + with: + apptainer-version: 1.3.4 + + - name: Read .nf-core.yml + id: read_yml + run: | + echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT" + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + + - name: Download the pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + run: | + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ + --container-cache-utilisation 'amend' \ + --download-configuration 'yes' + + - name: Inspect download + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" + + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + - name: Run the downloaded pipeline (stub run not supported) + id: run_pipeline + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" + + - name: Compare container image counts + id: count_comparison + run: | + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images > ./container_afterwards + diff ./container_initial ./container_afterwards + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi + + - name: Upload Nextflow logfile for debugging purposes + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: nextflow_logfile.txt + path: .nextflow.log* + include-hidden-files: true diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml new file mode 100644 index 00000000..a7b7663e --- /dev/null +++ b/.github/workflows/fix_linting.yml @@ -0,0 +1,85 @@ +name: Fix linting from a comment +on: + issue_comment: + types: [created] + +jobs: + fix-linting: + # Only run if comment is on a PR with the main repo, and if it contains the magic keywords + if: > + contains(github.event.comment.html_url, '/pull/') && + contains(github.event.comment.body, '@nf-core-bot fix linting') && + github.repository == 'nf-cmgg/preprocessing' + runs-on: ubuntu-latest + steps: + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + token: ${{ secrets.nf_core_bot_auth_token }} + + # indication that the linting is being fixed + - name: React on comment + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 + with: + comment-id: ${{ github.event.comment.id }} + reactions: eyes + + # Action runs on the issue comment, so we don't get the PR by default + # Use the gh cli to check out the PR + - name: Checkout Pull Request + run: gh pr checkout ${{ github.event.issue.number }} + env: + GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} + + - name: Install Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + + # Install and run prek + - name: Run prek + id: prek + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 + continue-on-error: true + + # indication that the linting has finished + - name: react if linting finished succesfully + if: steps.prek.outcome == 'success' + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 + with: + comment-id: ${{ github.event.comment.id }} + reactions: "+1" + + - name: Commit & push changes + id: commit-and-push + if: steps.prek.outcome == 'failure' + run: | + git config user.email "core@nf-co.re" + git config user.name "nf-core-bot" + git config push.default upstream + git add . + git status + git commit -m "[automated] Fix code linting" + git push + + - name: react if linting errors were fixed + id: react-if-fixed + if: steps.commit-and-push.outcome == 'success' + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 + with: + comment-id: ${{ github.event.comment.id }} + reactions: hooray + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 + with: + comment-id: ${{ github.event.comment.id }} + reactions: confused + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 + with: + issue-number: ${{ github.event.issue.number }} + body: | + @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. + See [CI log](https://github.com/nf-cmgg/preprocessing/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8738ffc9..277f12fb 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,30 +11,30 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Run prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" - name: Setup uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 @@ -46,7 +46,7 @@ jobs: run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -74,3 +74,21 @@ jobs: lint_log.txt lint_results.md PR_number.txt + + # Build a comment for the shared pr-comment.yml poster to publish on the PR + - name: Prepare PR comment + if: ${{ always() }} + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "lint" > pr-comment/header.txt + [ -f lint_results.md ] && cp lint_results.md pr-comment/comment.md || true + + - name: Upload PR comment artifact + if: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml deleted file mode 100644 index 5b0c24f7..00000000 --- a/.github/workflows/linting_comment.yml +++ /dev/null @@ -1,28 +0,0 @@ -name: nf-core linting comment -# This workflow is triggered after the linting action is complete -# It posts an automated comment to the PR, even if the PR is coming from a fork - -on: - workflow_run: - workflows: ["nf-core linting"] - -jobs: - test: - runs-on: ubuntu-latest - steps: - - name: Download lint results - uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 - with: - workflow: linting.yml - workflow_conclusion: completed - - - name: Get PR number - id: pr_number - run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - - - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - number: ${{ steps.pr_number.outputs.pr_number }} - path: linting-logs/lint_results.md diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 804208dd..25d754e9 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -9,7 +9,7 @@ on: - "**/*.svg" release: types: [published] - workflow_dispatch: null + workflow_dispatch: # Cancel if a newer run is started concurrency: @@ -41,7 +41,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 @@ -76,14 +76,14 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - 26.04.0 - - latest-everything + - "26.04.0" + - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 @@ -114,6 +114,22 @@ jobs: fi fi + # continue-on-error keeps latest-everything from failing the job, so it never shows up in + # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead; + # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those. + - name: Prepare PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + run: | + mkdir -p pr-comment-fragment + echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md + + - name: Upload PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment-fragment-${{ strategy.job-index }} + path: pr-comment-fragment/ + confirm-pass: needs: [nf-test] if: always() @@ -139,3 +155,44 @@ jobs: echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" echo "::endgroup::" + + - name: Download PR comment fragments + if: ${{ always() }} + uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + continue-on-error: true + with: + pattern: pr-comment-fragment-* + path: pr-comment-fragments + merge-multiple: true + + # Build a comment for the shared pr-comment.yml poster to publish on the PR. + # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported. + - name: Prepare PR comment + if: ${{ always() }} + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "nf-test" > pr-comment/header.txt + if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then + { + echo "## ❌ nf-test failed with latest Nextflow version" + echo "" + echo "> [!NOTE]" + echo "> Tests with Nextflow's latest version failed but it will not cause a CI workflow failure." + echo "> Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing." + echo "" + cat pr-comment-fragments/*.md + echo "" + echo "See the [full run](${RUN_URL}) for details." + } > pr-comment/comment.md + fi + + - name: Upload PR comment artifact + if: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/pr-comment.yml b/.github/workflows/pr-comment.yml new file mode 100644 index 00000000..ab7b59dd --- /dev/null +++ b/.github/workflows/pr-comment.yml @@ -0,0 +1,82 @@ +name: Post PR comment +# Shared, privileged comment poster. +# +# This is the single workflow that runs with a write token. It is triggered +# after any of the listed "producer" workflows complete on a pull request. +# Each producer runs untrusted PR code (if any) with a read-only token and +# uploads a `pr-comment` artifact describing the comment to post; this workflow +# only ever reads that plain-text artifact, so no PR code is executed here. +# +# Artifact contract (uploaded by producers under the name `pr-comment`): +# pr_number.txt - the pull request number +# header.txt - sticky-comment identifier (keeps comment types separate) +# comment.md - the Markdown body (omit the file to post nothing) + +on: + workflow_run: + workflows: + - "nf-core linting" + - "nf-core template version comment" + - "nf-core branch protection" + - "Run nf-test" + +permissions: + actions: read + contents: read + pull-requests: write + +jobs: + post-comment: + runs-on: ubuntu-latest + if: github.event.workflow_run.event == 'pull_request' + steps: + - name: Download PR comment artifact + uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 + with: + run_id: ${{ github.event.workflow_run.id }} + name: pr-comment + path: pr-comment + if_no_artifact_found: ignore + + - name: Read comment metadata + id: meta + run: | + echo "::group::Downloaded pr-comment contents" + ls -la pr-comment 2>/dev/null || echo "No pr-comment/ directory was downloaded." + echo "::endgroup::" + + if [ ! -d pr-comment ]; then + echo "No pr-comment artifact found; nothing to post." + exit 0 + fi + + if [ ! -f pr-comment/comment.md ]; then + echo "Artifact present but no comment.md; nothing to post." + exit 0 + fi + + pr_number=$(cat pr-comment/pr_number.txt) + header=$(cat pr-comment/header.txt) + echo "Found comment.md (header='$header', pr_number='$pr_number')." + + # Guard against anything unexpected ending up in the PR number. + case "$pr_number" in + ''|*[!0-9]*) + echo "Invalid PR number: '$pr_number'" + exit 1 + ;; + esac + + echo "pr_number=$pr_number" >> "$GITHUB_OUTPUT" + echo "header=$header" >> "$GITHUB_OUTPUT" + echo "post=true" >> "$GITHUB_OUTPUT" + echo "Will post comment to PR #${pr_number}." + + - name: Post PR comment + if: steps.meta.outputs.post == 'true' + uses: marocchino/sticky-pull-request-comment@5770ad5eb8f42dd2c4f34da00c94c5381e49af88 # v3.0.5 + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + number: ${{ steps.meta.outputs.pr_number }} + header: ${{ steps.meta.outputs.header }} + path: pr-comment/comment.md diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml deleted file mode 100644 index c3674af2..00000000 --- a/.github/workflows/release-announcements.yml +++ /dev/null @@ -1,75 +0,0 @@ -name: release-announcements -# Automatic release toot and tweet anouncements -on: - release: - types: [published] - workflow_dispatch: - -jobs: - toot: - runs-on: ubuntu-latest - steps: - - name: get topics and convert to hashtags - id: get_topics - run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT - - - uses: rzr/fediverse-action@master - with: - access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} - host: "mstdn.science" # custom host if not "mastodon.social" (default) - # GitHub event payload - # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release - message: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - - ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics - - send-tweet: - runs-on: ubuntu-latest - - steps: - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy - - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} - - bsky-post: - runs-on: ubuntu-latest - steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 - with: - post: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - env: - BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} - BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} - # diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml new file mode 100644 index 00000000..149e2851 --- /dev/null +++ b/.github/workflows/template-version-comment.yml @@ -0,0 +1,60 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: + pull_request: + +permissions: {} + +jobs: + check_template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core + + - name: Build PR comment if template is outdated + # The fork-controlled version is passed via the environment and only ever + # used as quoted shell data (never interpolated into a command), so it + # cannot be used for script injection. + env: + PR_VERSION: ${{ steps.read_yml.outputs['nf_core_version'] }} + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "template-version" > pr-comment/header.txt + + latest_version=$(nf-core --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n1) + + if [ -n "$PR_VERSION" ] && [ -n "$latest_version" ] && [ "$PR_VERSION" != "$latest_version" ]; then + cat > pr-comment/comment.md < [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${PR_VERSION}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). + EOF + fi + + - name: Upload PR comment artifact + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.gitignore b/.gitignore index dfd0273a..630cf3e3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ .nextflow* +.nf-test* work/ data/ results/ @@ -7,8 +8,6 @@ testing/ testing* *.pyc null/ -.nf-test* -test_fc .lineage/ # pixi environments .pixi/* diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index 363d5b1d..00000000 --- a/.gitpod.yml +++ /dev/null @@ -1,22 +0,0 @@ -image: nfcore/gitpod:latest -tasks: - - name: Update Nextflow and setup pre-commit - command: | - pre-commit install --install-hooks - nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS - -vscode: - extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh new file mode 100755 index 00000000..e9ba4f93 --- /dev/null +++ b/.hooks/block_pipeline_outdir.sh @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +# This hook is used to block commits if they include staged files inside a directory +# which also contains a subdirectory called `pipeline_info`. The purpose of this is to +# prevent users from inadvertently committing output from pipeline test runs inside the +# development directory. + +set -e + +status=0 +seen_dirs="" + +while IFS= read -r file; do + # The offending output bundle's root is the ancestor directory that has + # `pipeline_info` as an immediate child, so callers can restore it in one go. + if [[ "$file" == pipeline_info/* ]]; then + top_dir="pipeline_info" + elif [[ "$file" == */pipeline_info/* ]]; then + top_dir="${file%%/pipeline_info/*}" + else + top_dir="" + dir=$(dirname "$file") + while [[ "$dir" != "." && "$dir" != "/" ]]; do + if [[ -d "$dir/pipeline_info" ]]; then + top_dir="$dir" + break + fi + dir=$(dirname "$dir") + done + fi + + if [[ -n "$top_dir" ]]; then + echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file" + status=1 + case "$seen_dirs" in + *"|$top_dir|"*) ;; + *) + echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area." + seen_dirs="$seen_dirs|$top_dir|" + ;; + esac + fi +done < <(git diff --cached --name-only) + +exit "$status" diff --git a/.nf-core.yml b/.nf-core.yml index 28d8bd53..c419716d 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,42 +1,47 @@ +repository_type: pipeline + +nf_core_version: 4.1.0 + lint: - files_exist: - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awsfulltest.yml - - .github/workflows/awstest.yml - - CITATIONS.md + files_unchanged: - CODE_OF_CONDUCT.md - assets/nf-core-preprocessing_logo_light.png - - docs/CONTRIBUTING.md - - docs/images/nf-core-preprocessing_logo_dark.png - docs/images/nf-core-preprocessing_logo_light.png - files_unchanged: + - docs/images/nf-core-preprocessing_logo_dark.png - .github/ISSUE_TEMPLATE/bug_report.yml - .github/PULL_REQUEST_TEMPLATE.md + - assets/email_template.txt + - docs/README.md - .gitignore + - assets/multiqc_config.yaml + nextflow_config: + - manifest.name + - manifest.homePage + multiqc_config: false + files_exist: - CODE_OF_CONDUCT.md - - LICENSE + - docs/CONTRIBUTING.md - assets/nf-core-preprocessing_logo_light.png - - docs/README.md - - docs/images/nf-core-preprocessing_logo_dark.png - docs/images/nf-core-preprocessing_logo_light.png + - docs/images/nf-core-preprocessing_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml merge_markers: - bin/cmgg_genelists - .pixi/envs - multiqc_config: false - nextflow_config: false - schema_params: false # TMP template_strings: - bin/cmgg_genelists - nf_test_content: false -nf_core_version: 4.0.2 -repository_type: pipeline template: - author: Matthias De Smet, Nicolas Vannieuwkerke - description: Demultiplexing, adapter trimming, alignment, and coverage calculation for NGS data. - force: false - is_nfcore: false - name: preprocessing org: nf-cmgg + name: preprocessing + description: Demultiplexing, adapter trimming, alignment, and coverage calculation for NGS data. + author: Matthias De Smet, Nicolas Vannieuwkerke and the CMGG IT Team + version: 3.1.0 + force: true outdir: . - skip_features: ["fastqc"] - version: 3.0.2 + skip_features: + - fastqc + - seqera_platform + - gpu + is_nfcore: false diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d06777a8..e9503db1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.6.2 + - prettier@3.9.6 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -13,15 +13,38 @@ repos: exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ - id: end-of-file-fixer exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ + - id: check-added-large-files + args: [--maxkb=5000] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + .*\.snap$| + lib/nfcore_external_java_deps.jar$| + docs/.*\.(svg|pdf)$| + assets/.*$ + )$ + - id: check-merge-conflict + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.3.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' + args: ["-output", "json"] + - repo: local + hooks: + - id: block-pipeline-outdir + name: Prevent committing output from pipeline test runs to the pipeline code itself + entry: ./.hooks/block_pipeline_outdir.sh + language: script diff --git a/.vscode/settings.json b/.vscode/settings.json index af2d783f..a33b527c 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,4 +1,3 @@ { - "markdown.styles": ["public/vscode_markdown.css"], - "nextflow.telemetry.enabled": false + "markdown.styles": ["public/vscode_markdown.css"] } diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 00000000..2f665dca --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,28 @@ +# nf-cmgg/preprocessing + +This repository uses the nf-core pipeline template (`is_nfcore: false` in `.nf-core.yml`) in the nf-cmgg organisation. + +## nf-core instructions + +Follow [nf-core pipeline AGENTS.md](https://github.com/nf-core/agents/blob/main/resources/pipeline/AGENTS.md). Those rules apply here. Do not restate them in this file. + +## This repository + +- Use `pixi install` then `pixi shell` for development. `pixi.toml` provides nextflow, nf-core, nf-test, and prek. +- Institutional configs default to [nf-core/configs](https://github.com/nf-core/configs) via `params.custom_config_base`. If that URL contains `nf-cmgg`, `pipeline/preprocessing.config` is also loaded. +- Main analysis lives in `workflows/preprocessing.nf`. Pipeline-only code belongs in `modules/local/` and `subworkflows/local/`. +- Use `nf-core modules install` to add new modules. Remember to also amend citations across the repository. +- Use `nf-metro` to render custom workflow diagram based on the mermaid source in `docs/images/metro_map_light.md` and `docs/images/metro_map_dark.md`. +- Do not invent files that nf-core tools should generate. + +## After writing + +After any code or docs edit, run the deslop skill on the new diff. Strip extra comments, defensive noise, and style that does not match the surrounding files. Keep behaviour unchanged. + +After Nextflow code edits, run on the files you changed: + +``` +nextflow lint -format -sort-declarations -exclude ".nf-test" -exclude ".pixi" -exclude "modules/nf-core" -exclude "subworkflows/nf-core" -harshil-alignment . +``` + +Resolve reported issues. Do not format `modules/nf-core` or `subworkflows/nf-core`. diff --git a/CHANGELOG.md b/CHANGELOG.md index 3a589fd1..af6de121 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,36 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## Unreleased + +## 3.1.0 + +- Set default `split_fastq` parameter to 0, disabling FastQ splitting by default. +- Migrate `fgumi/extract` to a local process and add sorting. +- Improve and fix `fgumi/snapzipsort` process by piping data, optimizing sorting (`queryname::natural` and `template-coordinate`) and compression steps. +- Add configurable `fgumi extract` parameters for read structures and UMI extraction mode. +- Publish flowcell InterOp binaries under `InterOp/`. +- Add optional `sequencing_center` samplesheet field for BAM `@RG CN`. +- Allow single-end FASTQ samplesheet rows (`fastq_2` optional). +- Default typed institutional config params to nf-core/configs. +- Error when a BCL Convert `fastq_list.csv` Read1File is missing from demultiplexed FASTQs. +- Skip panel coverage when no gene lists remain after SeqCap filtering. +- Drop unused `fgumi_group_edits` meta; fgumi group always uses `--edits 1`. +- Pair split FASTP R1/R2 chunks by filename so mates stay together. +- Align paired FASTQs with BWA as separate mates instead of interleaved input. +- Fail DNA alignment when the requested aligner is not supported instead of dropping the sample. +- Keep UMI consensus filter/SNAP steps on the merged sample meta so they still run after fastp splitting. +- Omit empty FASTQ `CN`/`LB` read-group fields so they are not written as empty strings. +- Add support for Equus caballus genome (EquCab2) when the organism is specified in the sample metadata. +- Associate demultiplexed FASTQs with multiplexed `sampleinfo` rows using `readgroup.LB` when the same `samplename` appears in more than one library ([#169](https://github.com/nf-cmgg/preprocessing/issues/169)). Those libraries are published under `LIBRARY/SAMPLENAME`. +- Drop `Picard` modules and associated parameters in favor of `riker multi`, which is much more efficient and now run by default. +- Add `apple` profile to enable the use of Apple containers. +- Drop `hook_url` parameter. Notifications are now handled by the `nf-teams` plugin, which is enabled in `nextflow.config` and configured through a custom config. +- Drop `run_coverage` and add `qc_mode` parameter. Thorough coverage analysis is now included in the `qc_mode` parameter, which can be set to `basic` or `full`. Basic QC includes samtools flagstat, idxstats and mosdepth. Full QC includes samtools stats, samtools coverage, riker metrics and panel coverage in addition to basic QC. +- Revert default custom config to `nf-core` source +- Bump pipeline to nf-core template v4.1.0 +- Bump modules to latest versions + ## 3.0.2 - remove common plugins in favor of defining them in the nf-cmgg/configs, which will be used across all nf-cmgg pipelines. This allows for better version control and consistency across pipelines, as well as reducing the maintenance burden of keeping plugins up to date in multiple repositories. diff --git a/CITATIONS.md b/CITATIONS.md index 2a5a3059..05e90f37 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,13 +10,63 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +- [biobambam2](https://pubmed.ncbi.nlm.nih.gov/24927705/) + + > Tischler G, Leonard S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol Med. 2014 Jun 20;9:13. doi: 10.1186/1751-0473-9-13. PubMed PMID: 24927705; PubMed Central PMCID: PMC4077101. + +- [Bowtie 2](https://pubmed.ncbi.nlm.nih.gov/22388286/) + + > Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923. PubMed PMID: 22388286; PubMed Central PMCID: PMC3322381. + +- [BWA-MEM](https://arxiv.org/abs/1303.3997) + + > Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013. doi: 10.48550/arXiv.1303.3997. + +- [BWA-MEM2](https://ieeexplore.ieee.org/document/8820962) + + > Vasimuddin M, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2019, pp. 314-324. doi: 10.1109/IPDPS.2019.00041. + +- [DRAGMAP](https://github.com/Illumina/DRAGMAP) + +- [Falco](https://pubmed.ncbi.nlm.nih.gov/33552473/) + + > de Sena Brandine G, Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Res. 2021 Jan 27;8:1874. doi: 10.12688/f1000research.21142.2. PubMed PMID: 33552473; PubMed Central PMCID: PMC7845152. + +- [fastp](https://pubmed.ncbi.nlm.nih.gov/30423086/) + + > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281. + +- [fgumi](https://github.com/fulcrumgenomics/fgumi) + +- [mosdepth](https://pubmed.ncbi.nlm.nih.gov/29096012/) + + > Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699. PubMed PMID: 29096012; PubMed Central PMCID: PMC6030888. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) -> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + +- [MultiQC SAV](https://github.com/MultiQC/MultiQC_SAV) + +- [riker](https://github.com/fulcrumgenomics/riker) + +- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/) + + > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002. + +- [SNAP](https://arxiv.org/abs/1111.5572) + + > Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson D, Shenker S, Stoica I, Karp RM, Sittler T. Faster and More Accurate Sequence Alignment with SNAP. arXiv 2011. doi: 10.48550/arXiv.1111.5572. + +- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) + + > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905. + +- [strobealign](https://pubmed.ncbi.nlm.nih.gov/36581923/) + + > Sahlin K. Strobealign: flexible seed size enables ultra-fast and accurate read alignment. Genome Biol. 2022 Dec 29;23(1):260. doi: 10.1186/s13059-022-02831-7. PubMed PMID: 36581923; PubMed Central PMCID: PMC9798760. ## Software packaging/containerisation tools diff --git a/LICENSE b/LICENSE index 6406a806..d52aa1a9 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) CMGG ICT team +Copyright (c) The nf-cmgg/preprocessing team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index d6aca64a..9fab31e8 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,14 @@ # nf-cmgg/preprocessing -[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-cmgg/preprocessing) +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-cmgg/preprocessing) [![GitHub Actions CI Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml) -[![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-cmgg/preprocessing) ## Introduction @@ -20,20 +19,21 @@ The pipeline is built using Nextflow, a workflow tool to run tasks across multip Steps include: -- Demultiplexing using [`BCLconvert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html) +- Demultiplexing using [`BCL Convert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html) - Run QC using [`MultiQC SAV`](https://github.com/MultiQC/MultiQC_SAV) -- Read QC and trimming using [`fastp`](https://github.com/OpenGene/fastp) or [`falco`](https://github.com/smithlabcode/falco) -- Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq +- Read QC and adapter trimming using [`fastp`](https://github.com/OpenGene/fastp). Samples without a supported genome or with `aligner` set to `false` skip alignment and are QC'd with [`falco`](https://github.com/smithlabcode/falco) instead +- Alignment using [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobealign`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq +- UMI consensus (`call_consensus`) using [`fgumi`](https://github.com/fulcrumgenomics/fgbio) with SNAP - Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html) -- Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html) -- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollectHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics) -- QC aggregation using [`multiqc`](https://multiqc.info/) +- Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and, in `qc_mode: full`, [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html) +- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and, in `qc_mode: full`, [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html) and [`riker multi`](https://github.com/fulcrumgenomics/riker) +- QC aggregation using [`MultiQC`](https://multiqc.info/) - Fallback image description + nf-cmgg/preprocessing workflow overview ## Usage @@ -73,6 +73,8 @@ Then run `pixi shell` to enter the environment and start developing. nf-cmgg/preprocessing was originally written by the CMGG ICT team. +An extensive list of references for the tools used by the pipeline can be found in [`CITATIONS.md`](CITATIONS.md). + ## Support This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml deleted file mode 100644 index 8902b62a..00000000 --- a/assets/methods_description_template.yml +++ /dev/null @@ -1,29 +0,0 @@ -id: "nf-cmgg-preprocessing-methods-description" -description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "nf-cmgg/preprocessing Methods Description" -section_href: "https://github.com/nf-cmgg/preprocessing" -plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object -data: | -

Methods

-

Data was processed using nf-cmgg/preprocessing v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

-

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

- 
${workflow.commandLine}
-

${tool_citations}

-

References

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    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
    • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
    • -
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • -
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • - ${tool_bibliography} -
-
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Notes:
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    - ${nodoi_text} -
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • -
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • -
-
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 349aabe1..47799816 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-cmgg/preprocessing analysis pipeline. + This report has been generated by the nf-cmgg/preprocessing analysis pipeline. report_section_order: "nf-cmgg-preprocessing-methods-description": order: -1000 diff --git a/assets/schema_input.json b/assets/schema_input.json index 8f666f27..e0b9672b 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -22,23 +22,23 @@ "organism": { "meta": ["organism"], "type": "string", - "description": "Sample organism. Currently supported organisms include Homo sapiens, Mus musculus and Danio rerio", + "description": "Sample organism. Currently supported organisms include Homo sapiens, Mus musculus, Danio rerio and Equus caballus", "pattern": "^[a-zA-Z0-9_\\s]+$" }, "genome": { "meta": ["genome"], "type": "string", - "description": "Genome build. Currently supported genomes include GRCh38, GRCh38-noalt, GRCm39, GRCz11, hg38 and hg38-noalt", + "description": "Genome build. Currently supported genomes include EquCab2, GRCh38, GRCh38-noalt, GRCm39, GRCz11, hg38 and hg38-noalt", "pattern": "^[a-zA-Z0-9_-]+$", "default": null, - "enum": ["GRCh38", "GRCh38-noalt", "GRCm39", "GRCz11", "hg38", "hg38-noalt"] + "enum": ["hg38-noalt", "hg38", "GRCz11", "GRCm39", "GRCh38-noalt", "GRCh38", "EquCab2"] }, "aligner": { "meta": ["aligner"], - "type": ["string", "boolean"], + "type": ["string"], "description": "Aligner to use to align sample to the reference genome", - "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star", "false", false], - "default": "false" + "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star", ""], + "default": "" }, "markdup": { "meta": ["markdup"], @@ -53,6 +53,44 @@ "description": "Run markdup in UMI-aware mode. This applies to Samtools only and requires the UMI to be in the read name.", "default": false }, + "call_consensus": { + "meta": ["call_consensus"], + "type": "boolean", + "description": "Enable UMI-aware consensus processing through the fgumi branch.", + "default": false + }, + "fgumi_extract_mode": { + "meta": ["fgumi_extract_mode"], + "type": "string", + "enum": ["read_structures", "read_names"], + "default": "read_names", + "description": "UMI extraction mode for fgumi consensus. Use 'read_structures' for sequence-based extraction or 'read_names' to parse UMIs from FASTQ read names." + }, + "fgumi_read_structure_r1": { + "meta": ["fgumi_read_structure_r1"], + "type": "string", + "default": "+T", + "description": "Read structure for FASTQ read 1 when fgumi_extract_mode is 'read_structures'." + }, + "fgumi_read_structure_r2": { + "meta": ["fgumi_read_structure_r2"], + "type": "string", + "default": "+T", + "description": "Read structure for FASTQ read 2 when fgumi_extract_mode is 'read_structures'." + }, + "fgumi_simplex_min_reads": { + "meta": ["fgumi_simplex_min_reads"], + "type": "integer", + "default": 1, + "minimum": 1, + "description": "Minimum number of reads required per UMI family for fgumi simplex consensus generation." + }, + "fgumi_snap_ignore_mismatched_pairs": { + "meta": ["fgumi_snap_ignore_mismatched_pairs"], + "type": "boolean", + "default": true, + "description": "Pass -I to SNAP to ignore mismatched read IDs in paired-end input." + }, "skip_trimming": { "meta": ["skip_trimming"], "type": "boolean", @@ -83,17 +121,12 @@ "description": "Adapter sequence to trim from read 2", "default": null }, - "run_coverage": { - "meta": ["run_coverage"], - "type": "boolean", - "description": "Whether to run coverage analysis for the sample", - "default": true - }, - "disable_picard_metrics": { - "meta": ["disable_picard_metrics"], - "type": "boolean", - "description": "Whether to disable Picard metrics calculation. This can be used to speed up processing if Picard is not needed.", - "default": true + "qc_mode": { + "meta": ["qc_mode"], + "type": "string", + "enum": ["basic", "full"], + "description": "Whether to run full QC for the sample. Basic QC includes samtools flagstat, idxstats and mosdepth. Full QC includes samtools stats, samtools coverage, riker metrics and panel coverage in addition to basic QC.", + "default": "basic" }, "roi": { "meta": ["roi"], @@ -122,6 +155,12 @@ "pattern": "^[a-zA-Z0-9_-]+$", "description": "Sample library name" }, + "sequencing_center": { + "meta": ["sequencing_center"], + "type": "string", + "description": "Sequencing centre for the BAM @RG CN field", + "pattern": "^[a-zA-Z0-9_-]+$" + }, "lane": { "type": "integer", "meta": ["lane"], @@ -150,7 +189,7 @@ "type": "string", "format": "file-path", "pattern": "^\\S+\\.(json|yaml|yml)$", - "description": "JSON/YAML file with sample information, must contain fields 'samplename', 'organism' and 'tag'" + "description": "JSON/YAML file with sample information, must contain fields 'samplename', 'aligner', 'tag' and either 'genome' or 'organism'" }, "flowcell": { "type": "string", @@ -160,10 +199,10 @@ }, "anyOf": [ { - "required": ["id", "samplename", "organism", "aligner", "fastq_1", "fastq_2"] + "required": ["id", "samplename", "organism", "aligner", "fastq_1"] }, { - "required": ["id", "samplename", "genome", "aligner", "fastq_1", "fastq_2"] + "required": ["id", "samplename", "genome", "aligner", "fastq_1"] }, { "required": ["id", "samplesheet", "sample_info", "flowcell"] diff --git a/assets/schema_sampleinfo.json b/assets/schema_sampleinfo.json index 092cc130..70bc0457 100644 --- a/assets/schema_sampleinfo.json +++ b/assets/schema_sampleinfo.json @@ -26,6 +26,12 @@ "description": "Library name", "pattern": "^[a-zA-Z0-9_-]+$" }, + "sequencing_center": { + "meta": ["sequencing_center"], + "type": "string", + "description": "Sequencing centre for the BAM @RG CN field", + "pattern": "^[a-zA-Z0-9_-]+$" + }, "tag": { "meta": ["tag"], "type": "string", @@ -47,10 +53,10 @@ "genome": { "meta": ["genome"], "type": "string", - "description": "Genome build. Currently supported genomes include GRCh38, GRCh38-noalt, GRCm39, GRCz11, hg38 and hg38-noalt", + "description": "Genome build. Currently supported genomes include EquCab2, GRCh38, GRCh38-noalt, GRCm39, GRCz11, hg38 and hg38-noalt", "pattern": "^[a-zA-Z0-9_-]+$", "default": null, - "enum": ["GRCh38", "GRCh38-noalt", "GRCm39", "GRCz11", "hg38", "hg38-noalt"] + "enum": ["hg38-noalt", "hg38", "GRCz11", "GRCm39", "GRCh38-noalt", "GRCh38", "EquCab2"] }, "vivar_project": { "meta": ["vivar_project"], @@ -77,8 +83,8 @@ "meta": ["aligner"], "type": ["string", "boolean"], "description": "Aligner to use to align sample to the reference genome", - "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star", "false", false], - "default": "false" + "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star", ""], + "default": "" }, "markdup": { "meta": ["markdup"], @@ -93,6 +99,44 @@ "description": "Run markdup in UMI-aware mode. This applies to Samtools only and requires the UMI to be in the read name.", "default": false }, + "call_consensus": { + "meta": ["call_consensus"], + "type": "boolean", + "description": "Enable UMI-aware consensus processing through the fgumi branch.", + "default": false + }, + "fgumi_extract_mode": { + "meta": ["fgumi_extract_mode"], + "type": "string", + "enum": ["read_structures", "read_names"], + "default": "read_names", + "description": "UMI extraction mode for fgumi consensus. Use 'read_structures' for sequence-based extraction or 'read_names' to parse UMIs from FASTQ read names." + }, + "fgumi_read_structure_r1": { + "meta": ["fgumi_read_structure_r1"], + "type": "string", + "default": "+T", + "description": "Read structure for FASTQ read 1 when fgumi_extract_mode is 'read_structures'." + }, + "fgumi_read_structure_r2": { + "meta": ["fgumi_read_structure_r2"], + "type": "string", + "default": "+T", + "description": "Read structure for FASTQ read 2 when fgumi_extract_mode is 'read_structures'." + }, + "fgumi_simplex_min_reads": { + "meta": ["fgumi_simplex_min_reads"], + "type": "integer", + "default": 1, + "minimum": 1, + "description": "Minimum number of reads required per UMI family for fgumi simplex consensus generation." + }, + "fgumi_snap_ignore_mismatched_pairs": { + "meta": ["fgumi_snap_ignore_mismatched_pairs"], + "type": "boolean", + "default": true, + "description": "Pass -I to SNAP to ignore mismatched read IDs in paired-end input." + }, "skip_trimming": { "meta": ["skip_trimming"], "type": "boolean", @@ -123,17 +167,12 @@ "description": "Adapter sequence to trim from read 2", "default": null }, - "run_coverage": { - "meta": ["run_coverage"], - "type": "boolean", - "description": "Whether to run coverage analysis for the sample", - "default": true - }, - "disable_picard_metrics": { - "meta": ["disable_picard_metrics"], - "type": "boolean", - "description": "Whether to disable Picard metrics calculation. This can be used to speed up processing if Picard is not needed.", - "default": true + "qc_mode": { + "meta": ["qc_mode"], + "type": "string", + "enum": ["basic", "full"], + "description": "Whether to run full QC for the sample. Basic QC includes samtools flagstat, idxstats and mosdepth. Full QC includes samtools stats, samtools coverage, riker metrics and panel coverage in addition to basic QC.", + "default": "basic" }, "roi": { "meta": ["roi"], @@ -147,10 +186,10 @@ }, "anyOf": [ { - "required": ["samplename", "organism", "aligner", "tag"] + "required": ["samplename", "organism"] }, { - "required": ["samplename", "genome", "aligner", "tag"] + "required": ["samplename", "genome"] } ] } diff --git a/bin/cmgg_genelists b/bin/cmgg_genelists index 928cf7c3..d3f325c4 100755 Binary files a/bin/cmgg_genelists and b/bin/cmgg_genelists differ diff --git a/conf/base.config b/conf/base.config index 75abf893..2d01a916 100644 --- a/conf/base.config +++ b/conf/base.config @@ -41,6 +41,12 @@ process { withLabel: process_long { time = { 20.h * task.attempt } } + withLabel: process_low_memory { + memory = { 1.GB * task.attempt } + } + withLabel: process_high_memory { + memory = { 200.GB * task.attempt } + } withLabel: error_ignore { errorStrategy = 'ignore' } diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index c8184a2d..ae3f201f 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } -process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt' } } +process { withName: 'FASTP' { conda = 'modules/nf-core/fastp/.conda-lock/linux_amd64-bd-4df8d6c11b471bde_1.txt' } } +process { withName: 'FGUMI_EXTRACTSORT' { conda = 'modules/nf-core/fgumi/extract/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt' } } +process { withName: 'FGUMI_FILTER' { conda = 'modules/nf-core/fgumi/filter/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt' } } +process { withName: 'FGUMI_GROUP' { conda = 'modules/nf-core/fgumi/group/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt' } } +process { withName: 'FGUMI_MERGE' { conda = 'modules/nf-core/fgumi/merge/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt' } } +process { withName: 'FGUMI_SIMPLEX' { conda = 'modules/nf-core/fgumi/simplex/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } +process { withName: 'MULTIQCSAV' { conda = 'modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-9b10d606ce2f36b6_1.txt' } } +process { withName: 'STROBEALIGN' { conda = 'modules/nf-core/strobealign/.conda-lock/linux_amd64-bd-90eb6a088ad3d321_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index 2f7b575a..b33e8dd3 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } -process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-039d1ec6b47ba325_1.txt' } } +process { withName: 'FASTP' { conda = 'modules/nf-core/fastp/.conda-lock/linux_arm64-bd-95b49074d3fe9875_1.txt' } } +process { withName: 'FGUMI_EXTRACTSORT' { conda = 'modules/nf-core/fgumi/extract/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt' } } +process { withName: 'FGUMI_FILTER' { conda = 'modules/nf-core/fgumi/filter/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt' } } +process { withName: 'FGUMI_GROUP' { conda = 'modules/nf-core/fgumi/group/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt' } } +process { withName: 'FGUMI_MERGE' { conda = 'modules/nf-core/fgumi/merge/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt' } } +process { withName: 'FGUMI_SIMPLEX' { conda = 'modules/nf-core/fgumi/simplex/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } +process { withName: 'MULTIQCSAV' { conda = 'modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-077315907ed11315_1.txt' } } +process { withName: 'STROBEALIGN' { conda = 'modules/nf-core/strobealign/.conda-lock/linux_arm64-bd-be473d108d6e0fb8_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index 78d2a3f2..221f2512 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } -process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:644a84cef31cc4aa' } } +process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:1.3.6--4df8d6c11b471bde' } } +process { withName: 'FGUMI_EXTRACTSORT' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a' } } +process { withName: 'FGUMI_FILTER' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a' } } +process { withName: 'FGUMI_GROUP' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a' } } +process { withName: 'FGUMI_MERGE' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a' } } +process { withName: 'FGUMI_SIMPLEX' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } +process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9b10d606ce2f36b6' } } +process { withName: 'STROBEALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:90eb6a088ad3d321' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index cb309025..33220689 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } -process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:039d1ec6b47ba325' } } +process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:1.3.6--95b49074d3fe9875' } } +process { withName: 'FGUMI_EXTRACTSORT' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb' } } +process { withName: 'FGUMI_FILTER' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb' } } +process { withName: 'FGUMI_GROUP' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb' } } +process { withName: 'FGUMI_MERGE' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb' } } +process { withName: 'FGUMI_SIMPLEX' { container = 'community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } +process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:077315907ed11315' } } +process { withName: 'STROBEALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:be473d108d6e0fb8' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index a53b4e19..fffe4699 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } -process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4590c19f294469392d1bd2689eb9d4a06f18d20f64c5dbc0bbc17473c9941b4e/data' } } +process { withName: 'FASTP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d013aad5427d824afe472e6607ea47685ff0181f1fb09e52a179e0ec39e43e88/data' } } +process { withName: 'FGUMI_EXTRACTSORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' } } +process { withName: 'FGUMI_FILTER' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' } } +process { withName: 'FGUMI_GROUP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' } } +process { withName: 'FGUMI_MERGE' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' } } +process { withName: 'FGUMI_SIMPLEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } +process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c1311ac2bfb96d77487985fce321b25bbea85f574f9932b827ed6cafe7f75963/data' } } +process { withName: 'STROBEALIGN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/58/58b8968bb248307d133950891a33c9e569f5f1aa729ad997d8bb1311ec7f2589/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index 06c0dd3f..c56636a0 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } -process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b047611068a4009d62d8352e8bb4ab27fa993708a82c029f115e6758b2e44bec/data' } } +process { withName: 'FASTP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/42/42ea3a248c30a6eb0ab5d5ca35ce8b50aab6ca75e982d43420779214517a516b/data' } } +process { withName: 'FGUMI_EXTRACTSORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data' } } +process { withName: 'FGUMI_FILTER' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data' } } +process { withName: 'FGUMI_GROUP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data' } } +process { withName: 'FGUMI_MERGE' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data' } } +process { withName: 'FGUMI_SIMPLEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } +process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/05/053f6d8c55b57e04b654070a3bd6eaa90685590158019d35c16092d301b80cb1/data' } } +process { withName: 'STROBEALIGN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/54a576c51485cf7af3223084b2bfffabbe1c25c92c987ba564bb061ad0a16c89/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index fe83b990..08ab2cfb 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } -process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9ebe780f2738c655' } } +process { withName: 'FASTP' { container = 'oras://community.wave.seqera.io/library/fastp:1.3.6--63f52bbe4fa9aee1' } } +process { withName: 'FGUMI_EXTRACTSORT' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55' } } +process { withName: 'FGUMI_FILTER' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55' } } +process { withName: 'FGUMI_GROUP' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55' } } +process { withName: 'FGUMI_MERGE' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55' } } +process { withName: 'FGUMI_SIMPLEX' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } +process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:a26da1aa4e8d32a6' } } +process { withName: 'STROBEALIGN' { container = 'oras://community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:38afc784dff2496a' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index fffe6e07..49627527 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -1,2 +1,9 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } -process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:fc57bb53140baade' } } +process { withName: 'FASTP' { container = 'oras://community.wave.seqera.io/library/fastp:1.3.6--469416be288311d1' } } +process { withName: 'FGUMI_EXTRACTSORT' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b' } } +process { withName: 'FGUMI_FILTER' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b' } } +process { withName: 'FGUMI_GROUP' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b' } } +process { withName: 'FGUMI_MERGE' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b' } } +process { withName: 'FGUMI_SIMPLEX' { container = 'oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } +process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:d1ed21d66511158d' } } +process { withName: 'STROBEALIGN' { container = 'oras://community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:90ad219a62d4fc12' } } diff --git a/conf/igenomes.config b/conf/igenomes.config index 928c49e0..f7de5034 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -10,110 +10,88 @@ params.genomes = [ GRCh38: [ - // Genome reference - fai : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.fai", - fasta : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna", - dict : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.dict", - gtf : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf", - - // Aligner reference - bowtie2 : "${params.igenomes_base}/Hsapiens/GRCh38/bowtie2", - bwamem : "${params.igenomes_base}/Hsapiens/GRCh38/bwa", - bwamem2 : "${params.igenomes_base}/Hsapiens/GRCh38/bwamem2", - dragmap : "${params.igenomes_base}/Hsapiens/GRCh38/dragmap", - snap : "${params.igenomes_base}/Hsapiens/GRCh38/snapaligner", - star : "${params.igenomes_base}/Hsapiens/GRCh38/star", - - // ROI's - roi_copgt : "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_coPGT-M_analyses_ROI_v1.bed", - roi_wes : "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v7.bed", + fai: "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.fai", + fasta: "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna", + dict: "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.dict", + gtf: "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf", + bowtie2: "${params.igenomes_base}/Hsapiens/GRCh38/bowtie2", + bwamem: "${params.igenomes_base}/Hsapiens/GRCh38/bwa", + bwamem2: "${params.igenomes_base}/Hsapiens/GRCh38/bwamem2", + dragmap: "${params.igenomes_base}/Hsapiens/GRCh38/dragmap", + snap: "${params.igenomes_base}/Hsapiens/GRCh38/snapaligner", + star: "${params.igenomes_base}/Hsapiens/GRCh38/star", + roi_copgt: "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_coPGT-M_analyses_ROI_v1.bed", + roi_wes: "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v7.bed", ], 'GRCh38-noalt': [ - // Genome reference - fai : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/seq/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.fai", - fasta : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/seq/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.fna", - dict : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/seq/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.dict", - - // Aligner reference - bowtie2 : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/bowtie2/", - bwa : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/bwa/", - bwamem2 : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/bwamem2/", - dragmap : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/dragmap/", - snap : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/snapaligner/", - - // WCX references - wisecondorx : "${params.igenomes_base}/Hsapiens/GRCh38-noalt/wisecondorx/", + fai: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/seq/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.fai", + fasta: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/seq/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.fna", + dict: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/seq/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.dict", + bowtie2: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/bowtie2/", + bwa: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/bwa/", + bwamem2: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/bwamem2/", + dragmap: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/dragmap/", + snap: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/snapaligner/", + wisecondorx: "${params.igenomes_base}/Hsapiens/GRCh38-noalt/wisecondorx/", ], GRCm39: [ - // Genome reference - fai : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna.fai", - fasta : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna", - dict : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.dict", - gtf : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.gtf", - - // Aligner reference - bowtie2 : "${params.igenomes_base}/Mmusculus/GRCm39/bowtie2", - bwamem : "${params.igenomes_base}/Mmusculus/GRCm39/bwa", - bwamem2 : "${params.igenomes_base}/Mmusculus/GRCm39/bwamem2", - dragmap : "${params.igenomes_base}/Mmusculus/GRCm39/dragmap", - snap : "${params.igenomes_base}/Mmusculus/GRCm39/snapaligner", - star : "${params.igenomes_base}/Mmusculus/GRCm39/star", + fai: "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna.fai", + fasta: "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna", + dict: "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.dict", + gtf: "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.gtf", + bowtie2: "${params.igenomes_base}/Mmusculus/GRCm39/bowtie2", + bwamem: "${params.igenomes_base}/Mmusculus/GRCm39/bwa", + bwamem2: "${params.igenomes_base}/Mmusculus/GRCm39/bwamem2", + dragmap: "${params.igenomes_base}/Mmusculus/GRCm39/dragmap", + snap: "${params.igenomes_base}/Mmusculus/GRCm39/snapaligner", + star: "${params.igenomes_base}/Mmusculus/GRCm39/star", ], mm10: [ - // Genome reference - fai : "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa.fai", - fasta : "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa", - dict : "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.dict", - gtf : "${params.igenomes_base}/Mmusculus/mm10/seq/Mus_musculus.GRCm38.102.chr.gtf", - - // Aligner reference - bowtie2 : "${params.igenomes_base}/Mmusculus/mm10/bowtie2", - bwamem : "${params.igenomes_base}/Mmusculus/mm10/bwa", - bwamem2 : "${params.igenomes_base}/Mmusculus/mm10/bwamem2", - dragmap : "${params.igenomes_base}/Mmusculus/mm10/dragmap", - snap : "${params.igenomes_base}/Mmusculus/mm10/snapaligner", - star : "${params.igenomes_base}/Mmusculus/mm10/star", + fai: "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa.fai", + fasta: "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa", + dict: "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.dict", + gtf: "${params.igenomes_base}/Mmusculus/mm10/seq/Mus_musculus.GRCm38.102.chr.gtf", + bowtie2: "${params.igenomes_base}/Mmusculus/mm10/bowtie2", + bwamem: "${params.igenomes_base}/Mmusculus/mm10/bwa", + bwamem2: "${params.igenomes_base}/Mmusculus/mm10/bwamem2", + dragmap: "${params.igenomes_base}/Mmusculus/mm10/dragmap", + snap: "${params.igenomes_base}/Mmusculus/mm10/snapaligner", + star: "${params.igenomes_base}/Mmusculus/mm10/star", ], GRCz11: [ - // Genome reference - fai : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna.fai", - fasta : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna", - dict : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.dict", - gtf : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.gtf", - - // Aligner reference - bowtie2 : "${params.igenomes_base}/Drerio/GRCz11/bowtie2", - bwamem : "${params.igenomes_base}/Drerio/GRCz11/bwa", - bwamem2 : "${params.igenomes_base}/Drerio/GRCz11/bwamem2", - dragmap : "${params.igenomes_base}/Drerio/GRCz11/dragmap", - snap : "${params.igenomes_base}/Drerio/GRCz11/snapaligner", - star : "${params.igenomes_base}/Drerio/GRCz11/star", + fai: "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna.fai", + fasta: "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna", + dict: "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.dict", + gtf: "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.gtf", + bowtie2: "${params.igenomes_base}/Drerio/GRCz11/bowtie2", + bwamem: "${params.igenomes_base}/Drerio/GRCz11/bwa", + bwamem2: "${params.igenomes_base}/Drerio/GRCz11/bwamem2", + dragmap: "${params.igenomes_base}/Drerio/GRCz11/dragmap", + snap: "${params.igenomes_base}/Drerio/GRCz11/snapaligner", + star: "${params.igenomes_base}/Drerio/GRCz11/star", ], - // Legacy bcbio references hg38: [ - fai : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa.fai", - fasta : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa", - dict : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.dict", - gtf : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.gtf", - - bowtie2 : "${params.igenomes_base}/Hsapiens/hg38/bowtie2", - bwamem : "${params.igenomes_base}/Hsapiens/hg38/bwa", - bwamem2 : "${params.igenomes_base}/Hsapiens/hg38/bwamem2", - dragmap : "${params.igenomes_base}/Hsapiens/hg38/dragmap", - snap : "${params.igenomes_base}/Hsapiens/hg38/snapaligner", - star : "${params.igenomes_base}/Hsapiens/hg38/star", + fai: "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa.fai", + fasta: "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa", + dict: "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.dict", + gtf: "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.gtf", + bowtie2: "${params.igenomes_base}/Hsapiens/hg38/bowtie2", + bwamem: "${params.igenomes_base}/Hsapiens/hg38/bwa", + bwamem2: "${params.igenomes_base}/Hsapiens/hg38/bwamem2", + dragmap: "${params.igenomes_base}/Hsapiens/hg38/dragmap", + snap: "${params.igenomes_base}/Hsapiens/hg38/snapaligner", + star: "${params.igenomes_base}/Hsapiens/hg38/star", ], 'hg38-noalt': [ - fai : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa.fai", - fasta : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa", - dict : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.dict", - gtf : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.gtf", - - bowtie2 : "${params.igenomes_base}/Hsapiens/hg38-noalt/bowtie2", - bwamem : "${params.igenomes_base}/Hsapiens/hg38-noalt/bwa", - bwamem2 : "${params.igenomes_base}/Hsapiens/hg38-noalt/bwamem2", - dragmap : "${params.igenomes_base}/Hsapiens/hg38-noalt/dragmap", - snap : "${params.igenomes_base}/Hsapiens/hg38-noalt/snapaligner", - star : "${params.igenomes_base}/Hsapiens/hg38-noalt/star", + fai: "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa.fai", + fasta: "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa", + dict: "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.dict", + gtf: "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.gtf", + bowtie2: "${params.igenomes_base}/Hsapiens/hg38-noalt/bowtie2", + bwamem: "${params.igenomes_base}/Hsapiens/hg38-noalt/bwa", + bwamem2: "${params.igenomes_base}/Hsapiens/hg38-noalt/bwamem2", + dragmap: "${params.igenomes_base}/Hsapiens/hg38-noalt/dragmap", + snap: "${params.igenomes_base}/Hsapiens/hg38-noalt/snapaligner", + star: "${params.igenomes_base}/Hsapiens/hg38-noalt/star", ], ] diff --git a/conf/modules.config b/conf/modules.config index 95978df0..264183a6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -32,7 +32,7 @@ process { ext.args = { [ params.split_fastq > 0 ? "--split_by_lines ${params.split_fastq * 4}" : '', - meta.skip_trimming ? "--disable_adapter_trimming" : "--detect_adapter_for_pe", + meta.skip_trimming ? "--disable_adapter_trimming" : (meta.single_end ? "" : "--detect_adapter_for_pe"), meta.trim_front > 0 ? "--trim_front1 ${meta.trim_front}" : "", meta.trim_tail > 0 ? "--trim_tail1 ${meta.trim_tail}" : "", meta.adapter_R1 ? "--adapter_sequence ${meta.adapter_R1}" : "", @@ -75,7 +75,6 @@ process { ext.args = { [ "-K 100000000", - "-p", "-v 3", "-Y", "-c 250", @@ -231,9 +230,125 @@ process { } } - // coverage + //// FGUMI extract/sort + withName: '.*FGUMI_EXTRACTSORT' { + ext.prefix = { "${meta.id}.fgumi.unmapped" } + ext.args = { + [ + "--read-group-id ${meta.readgroup?.get('ID') ? meta.readgroup.get('ID') : meta.id}", + meta.readgroup?.PL ? "--platform ${meta.readgroup.get('PL')}" : "", + meta.readgroup?.PU ? "--platform-unit \"${meta.readgroup.get('PU')}\"" : "", + meta.readgroup?.PM ? "--platform-model \"${meta.readgroup.get('PM')}\"" : "", + meta.readgroup?.CN ? "--sequencing-center \"${meta.readgroup.get('CN')}\"" : "", + meta.readgroup?.PI ? "--predicted-insert-size ${meta.readgroup.get('PI')}" : "", + meta.readgroup?.DS ? "--description \"${meta.readgroup.get('DS')}\"" : "", + meta.readgroup?.DT ? "--run-date \"${meta.readgroup.get('DT')}\"" : "", + meta.fgumi_extract_mode == "read_names" ? "--extract-umis-from-read-names" : "", + meta.fgumi_extract_mode == "read_structures" ? "--read-structures ${meta.fgumi_read_structure_r1} ${meta.fgumi_read_structure_r2}" : "" + ].join(" ").trim() + } + ext.args2 = { + ["--order queryname::natural"].join(" ").trim() + } + } + + //// SNAP | sort | zipper | sort + withName: RAW_FGUMI_SNAPZIPSORT { + ext.prefix = { "${meta.id}.fgumi" } + // SNAP + ext.args = { + [ + "-b-", + "-sm 20", + meta.fgumi_snap_ignore_mismatched_pairs ? "-I" : "", + "-hc-", + "-S id", + "-sa", + "-xf 2", + meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "", + ].join(" ").trim() + } + // Sort + // Use natural queryname ordering so mapped and unmapped read-name order stays consistent for fgumi zipper. + ext.args2 = { + [ + "--order queryname::natural", + "--compression-level 0" + ].join(" ").trim() + } + // Zipper + ext.args3 = { + ["--compression-level 0"].join(" ").trim() + } + // Final Sort + ext.args4 = { + [ + "--order template-coordinate", + "--key-types mi", + ].join(" ").trim() + } + } + + //// FGUMI group (step 4) + withName: '.*FGUMI_GROUP' { + ext.prefix = { "${meta.id}.fgumi.group" } + ext.args = { + ["--edits 1", "--max-memory ${task.memory.toGiga() / task.cpus}G"].join(" ").trim() + } + } + + //// FGUMI simplex (step 5) + withName: '.*FGUMI_SIMPLEX' { + ext.prefix = { "${meta.id}.fgumi.simplex" } + ext.args = { "--max-memory ${task.memory.toGiga() / task.cpus}G" } + } + + //// FGUMI filter + coordinate sort/index (step 7) + withName: '.*FGUMI_FILTER' { + ext.prefix = { "${meta.id}.fgumi.filter" } + ext.args = { "--max-memory ${task.memory.toGiga() / task.cpus}G" } + } + + //// FGUMI consensus alignment (step 8) + //// SNAP | sort | zipper | sort + withName: UMI_FGUMI_SNAPZIPSORT { + ext.prefix = { "${meta.id}.fgumi" } + // SNAP + ext.args = { + [ + "-b-", + "-sm 20", + meta.fgumi_snap_ignore_mismatched_pairs ? "-I" : "", + "-hc-", + "-S id", + "-sa", + "-xf 2", + meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "", + ].join(" ").trim() + } + // Sort + // Use natural queryname ordering so mapped and unmapped read-name order stays consistent for fgumi zipper. + ext.args2 = { + [ + "--order queryname::natural", + "--compression-level 0", + ].join(" ").trim() + } + // Zipper + ext.args3 = { + ["--compression-level 0"].join(" ").trim() + } + // Final Sort + ext.args4 = { + [ + "--order coordinate" + ].join(" ").trim() + } + } + + // QC //// Mosdepth - withName: '.*COVERAGE:MOSDEPTH' { + withName: '.*BAM_QC:MOSDEPTH' { cpus = 4 memory = { 4.GB * task.attempt } ext.args = [ @@ -243,27 +358,25 @@ process { ].join(" ").trim() } - //// Samtools coverage - withName: '.*COVERAGE:SAMTOOLS_COVERAGE' { - cpus = 1 - memory = 1.GB - ext.prefix = { "${meta.id}.coverage" } - } - - // QC - + //// Samtools/* withName: '.*BAM_QC:SAMTOOLS_.*$' { cpus = 1 memory = 1.GB } - //// Picard - withName: '.*BAM_QC:PICARD_.*$' { - cpus = 1 - memory = { 16.GB * task.attempt } - ext.args = "--MAX_RECORDS_IN_RAM 50000000" + //// Samtools/coverage + withName: '.*BAM_QC:SAMTOOLS_COVERAGE' { + cpus = 1 + memory = 1.GB + ext.prefix = { "${meta.id}.coverage" } + } + + //// Riker/multi + withName: '.*BAM_QC:RIKER_MULTI' { + ext.args = { "--tools alignment basic gcbias isize" + (meta.roi ? " hybcap" : " wgs") + (meta.sample_type == "RNA" ? " rna" : "") } } + //// MD5SUM withName: '.*MD5SUM' { cpus = 1 memory = 128.MB @@ -282,7 +395,6 @@ process { } } withName: '.*MULTIQC' { - container = "quay.io/cmgg/multiqc_cmgg:0.0.5-multiqc-v1.33" cpus = 1 memory = 4.GB ext.prefix = { params.multiqc_title ? "${params.multiqc_title}_${meta.id}" : "${meta.id}" } @@ -298,5 +410,5 @@ process { env { // Set TMPDIR for all modules - TMPDIR = "\$PWD" + TMPDIR = "\$PWD" } diff --git a/conf/test.config b/conf/test.config index 8b6c7486..6218fa63 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,7 +16,7 @@ params { // Input data input = "${projectDir}/tests/inputs/test.yml" - igenomes_base = "s3://reference-data/genomes" + custom_config_base = "" } process { @@ -28,3 +28,10 @@ process { } includeConfig "../tests/config/igenomes_test.config" + +aws { + client { + endpoint = 'https://s3.ugent.be' + s3PathStyleAccess = true + } +} diff --git a/docs/images/metro_map_dark.md b/docs/images/metro_map_dark.md index 65349f39..b3c4b3b6 100644 --- a/docs/images/metro_map_dark.md +++ b/docs/images/metro_map_dark.md @@ -39,7 +39,7 @@ graph TD SAMTOOLS_COV -->|qc| MULTIQC_LIBRARY CRAM_OUT -->|qc| SAMTOOLS_QC - CRAM_OUT -->|qc| PICARD + CRAM_OUT -->|qc| RIKER SAMTOOLS_QC -->|qc| MULTIQC_LIBRARY - PICARD -->|qc| MULTIQC_LIBRARY + RIKER -->|qc| MULTIQC_LIBRARY ``` diff --git a/docs/images/metro_map_dark.svg b/docs/images/metro_map_dark.svg index 0f452bc5..8b88840b 100644 --- a/docs/images/metro_map_dark.svg +++ b/docs/images/metro_map_dark.svg @@ -87,7 +87,7 @@ MOSDEPTH SAMTOOLS_COV SAMTOOLS_QC -PICARD +RIKER MULTIQC_LIBRARY diff --git a/docs/images/metro_map_light.md b/docs/images/metro_map_light.md index 5cd6a5b0..eb93ce46 100644 --- a/docs/images/metro_map_light.md +++ b/docs/images/metro_map_light.md @@ -39,7 +39,7 @@ graph TD SAMTOOLS_COV -->|qc| MULTIQC_LIBRARY CRAM_OUT -->|qc| SAMTOOLS_QC - CRAM_OUT -->|qc| PICARD + CRAM_OUT -->|qc| RIKER SAMTOOLS_QC -->|qc| MULTIQC_LIBRARY - PICARD -->|qc| MULTIQC_LIBRARY + RIKER -->|qc| MULTIQC_LIBRARY ``` diff --git a/docs/images/metro_map_light.svg b/docs/images/metro_map_light.svg index ac3be697..c6487f66 100644 --- a/docs/images/metro_map_light.svg +++ b/docs/images/metro_map_light.svg @@ -92,7 +92,7 @@ MOSDEPTH SAMTOOLS_COV SAMTOOLS_QC -PICARD +RIKER MULTIQC_LIBRARY diff --git a/docs/output.md b/docs/output.md index 119dd95e..7b2bfa32 100644 --- a/docs/output.md +++ b/docs/output.md @@ -10,42 +10,21 @@ The directories listed below will be created in the results directory after the ### Sample information -A separate directory will be created in the output directory for each sample containing all output files for that sample. If a library name is given in the samplesheet, the sample directories will be nested within a library directory. +Each sample's files are published under `SAMPLENAME`, or `LIBRARY/SAMPLENAME` when `library` is set. The same samplename in more than one library is published under each library so the files do not overwrite each other. Which files appear depends on `qc_mode`, whether alignment ran, and whether the sample is DNA or RNA.
Output files -- `SAMPLE` - - `SAMPLE.CollectHsMetrics.coverage_metrics`: The coverage metrics calculated by `picard CollectHsMetrics` - - `SAMPLE.CollectMultipleMetrics.alignment_summary_metrics`: The alignment summary metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.base_distribution_by_cycle_metrics`: The base distribution by cycle metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.base_distribution_by_cycle.pdf`: PDF file containing the base distribution by cycle metrics - - `SAMPLE.CollectMultipleMetrics.quality_by_cycle_metrics`: The quality by cycle metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.quality_by_cycle.pdf`: PDF file containing the quality by cycle metrics - - `SAMPLE.CollectMultipleMetrics.quality_distribution_metrics`: The quality by distribution metrics calculated by `picard CollectMultipleMetrics` - - `SAMPLE.CollectMultipleMetrics.quality_distribution.pdf`: PDF file containing the quality distribution metrics - - `SAMPLE.CollectMultipleMetrics.read_length_histogram.pdf`: A histogram detailing the read lengths made with `picard CollectMultipleMetrics` - - `SAMPLE.coverage.txt`: The coverage metrics calculated by `samtools coverage` - - `SAMPLE.cram`: The CRAM file generated by the aligner - - `SAMPLE.cram.crai`: The index of the CRAM file - - `SAMPLE.cram.md5`: The md5sum of the CRAM file - - `SAMPLE.duplicate_metrics.txt`: The duplicate metrics calculated by `samtools markdup` - - `SAMPLE.fastp.html`: The HTML file visualising the metrics calculated by `fastp` - - `SAMPLE.fastp.json`: The JSON file containing the metrics calculated by `fastp` - - `SAMPLE.flagstat`: The quality control metrics calculated by `samtools flagstat` - - `SAMPLE.idxstats`: The quality control metrics calculated by `samtools idxstats` - - `SAMPLE.mosdepth.global.dist.txt`: The global read distribution metrics calculated by `mosdepth` - - `SAMPLE.mosdepth.region.dist.txt`: The regional read distribution metrics calculated by `mosdepth` (only when a ROI BED file has been given) - - `SAMPLE.mosdepth.summary.txt`: The summary of the `mosdepth` metrics - - `SAMPLE.per-base.bed.gz`: The per-base depth calculated by `mosdepth` - - `SAMPLE.per-base.bed.gz.csi`: The index of the per-base depth BED file - - `SAMPLE.quantized.bed.gz`: The quantized BED file, showing how well covered each genomic region is, calculated by `mosdepth` - - `SAMPLE.quantized.bed.gz.csi`: The index of the quantized BED file - - `SAMPLE.regions.bed.gz`: The regional BED file, showing how well covered the requested regions are, calculated by `mosdepth` (only when a ROI BED file has been given) - - `SAMPLE.regions.bed.gz.csi`: The index of the regional BED file - - `SAMPLE.stats`: General statistics for the sample - - `multiqc/`: Directory containing the MultiQC report for the sample or library -
+- `SAMPLENAME/` or `LIBRARY/SAMPLENAME/` + - `SAMPLENAME.cram`, `.cram.crai`, `.cram.md5` for aligned samples + - `SAMPLENAME.duplicate_metrics.txt` from `bamsormadup` or `samtools markdup` + - fastp HTML/JSON for aligned samples + - Falco reports and untrimmed FASTQ when alignment is skipped (`aligner: false` or unsupported genome) + - STAR splice junction files for RNA samples + - `SAMPLENAME.flagstat`, `SAMPLENAME.idxstats`, and mosdepth files (region files only with an ROI BED) + - `qc_mode: full` also writes `samtools coverage`, `samtools stats`, riker metrics, and panel coverage when gene lists are provided + + ### Extra outputs for flowcell inputs @@ -54,8 +33,9 @@ Some additional files will be created when a flowcell input has been used.
Output files -- `InterOp/`: Directory containing `bins` for each sample -- `Reports/`: Quality control reports for the flowcell run +- `InterOp/`: InterOp binary files from the flowcell +- `Reports/`: BCL Convert reports (`Reports/L00/` when a lane is set) +- `Logs/`: BCL Convert logs (`Logs/L00/` when a lane is set)
@@ -64,16 +44,15 @@ Some additional files will be created when a flowcell input has been used.
Output files -- `multiqc/` +- `LIBRARY/multiqc/` (or `multiqc/` when no library is set) - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - `multiqc_plots/`: directory containing static images from the report in various formats. +- `multiqc/`: MultiQC SAV reports for flowcell runs
-[MultiQC](https://seqera.io/multiqc/) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. - -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . +[MultiQC](https://seqera.io/multiqc/) generates an HTML report per library (or a single `multiqc/` report when no library is set). Flowcell runs also produce a MultiQC SAV report under `multiqc/`. Software versions are included in the MultiQC output. For more information about how to use MultiQC reports, see . ### Pipeline information @@ -81,8 +60,8 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ Output files - `pipeline_info/` - - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.mmd`. - - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameters are used when running the pipeline. + - Reports generated by Nextflow: `execution_report_.html`, `execution_timeline_.html`, `execution_trace_.txt` and `pipeline_dag_.mmd`. + - Reports generated by the pipeline: `pipeline_report.html` and `pipeline_report.txt`. These are only written when `--email` / `--email_on_fail` is used. diff --git a/docs/parameters.md b/docs/parameters.md index 0f7220fc..5f0ee128 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -8,11 +8,10 @@ Define where the pipeline should find input data and save output data. | Parameter | Description | Type | Default | Required | Hidden | | --------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------- | ------- | -------- | ------ | -| `input` | Path to comma-separated or yaml file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location.
| `string` | | True | | +| `input` | Path to a file containing information about the samples in the experiment. Supported formats are CSV, TSV, YAML, and JSON.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location.
| `string` | | True | | | `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | | True | | -| `email` | Email address for completion summary.
HelpSet this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
| `` | | | | +| `email` | Email address for completion summary.
HelpSet this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the pipeline exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
| `string` | | | | | `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` | | | | -| `genomes` | | `object` | | | True | ## Pipeline options @@ -21,18 +20,27 @@ Define where the pipeline should find input data and save output data. | `split_fastq` | Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.
HelpUse the tool FastP to split FASTQ file by number of reads. This parallelizes across fastq file shards speeding up mapping. Note although the minimum value is 250 reads, if you have fewer than 250 reads a single FASTQ shard will still be created.
| `integer` | 100000000 | | | | `genelists` | Directory containing gene list bed files for granular coverage analysis | `string` | None | | | +## Reference genome options + +Reference genome related files and options required for the workflow. + +| Parameter | Description | Type | Default | Required | Hidden | +| --------------- | ----------------------------------------------------------------------------- | -------- | ----------- | -------- | ------ | +| `genomes` | Map of genome keys to reference files. Populated from `conf/igenomes.config`. | `object` | | | True | +| `igenomes_base` | The base path to the igenomes reference files | `string` | /references | | True | + ## Institutional config options Parameters used to describe centralised config profiles. These should not be edited. -| Parameter | Description | Type | Default | Required | Hidden | -| ---------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------- | ------------------------------------------------------ | -------- | ------ | -| `custom_config_version` | Git commit id for Institutional configs. | `string` | main | | True | -| `custom_config_base` | Base directory for custom configs.
HelpIf you're running offline, Nextflow will not be able to fetch the custom config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
| `string` | https://raw.githubusercontent.com/nf-cmgg/configs/main | | True | -| `config_profile_name` | Institutional config name. | `string` | | | True | -| `config_profile_description` | Institutional config description. | `string` | | | True | -| `config_profile_contact` | Institutional config contact information. | `string` | | | True | -| `config_profile_url` | Institutional config URL link. | `string` | | | True | +| Parameter | Description | Type | Default | Required | Hidden | +| ---------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------- | -------------------------------------------------------- | -------- | ------ | +| `custom_config_version` | Git commit id for Institutional configs. | `string` | master | | True | +| `custom_config_base` | Base directory for Institutional configs.
HelpIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
| `string` | https://raw.githubusercontent.com/nf-core/configs/master | | True | +| `config_profile_name` | Institutional config name. | `string` | | | True | +| `config_profile_description` | Institutional config description. | `string` | | | True | +| `config_profile_contact` | Institutional config contact information. | `string` | | | True | +| `config_profile_url` | Institutional config URL link. | `string` | | | True | ## Generic options @@ -46,16 +54,12 @@ Less common options for the pipeline, typically set in a config file. | `plaintext_email` | Send plain-text email instead of HTML. | `boolean` | | | True | | `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB | | True | | `monochrome_logs` | Do not use coloured log outputs. | `boolean` | | | True | -| `hook_url` | Incoming hook URL for messaging service
HelpIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
| `string` | | | True | | `multiqc_config` | Custom config file to supply to MultiQC. | `string` | | | True | | `multiqc_logo` | Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file | `string` | | | True | -| `multiqc_methods_description` | Custom MultiQC yaml file containing HTML including a methods description. | `string` | | | | | `validate_params` | Boolean whether to validate parameters against the schema at runtime | `boolean` | True | | True | +| `modules_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/nf-core/test-datasets/ | | True | | `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/nf-core/test-datasets/ | | True | | `trace_report_suffix` | Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss. | `string` | | | True | | `help` | Display the help message. | `['boolean', 'string']` | | | | | `help_full` | Display the full detailed help message. | `boolean` | | | | | `show_hidden` | Display hidden parameters in the help message (only works when --help or --help_full are provided). | `boolean` | | | | -| `igenomes_base` | Directory / URL base for iGenomes references. | `string` | /references/ | | True | -| `igenomes_ignore` | Do not load the iGenomes reference config.
HelpDo not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
| `boolean` | | | True | -| `genome` | Name of iGenomes reference.
HelpIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`.

See the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.
| `string` | | | | diff --git a/docs/usage.md b/docs/usage.md index f59c809a..8ff896a1 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -2,17 +2,15 @@ Parameter documentation can be found [here](parameters.md) -## Introduction - ## Samplesheet input -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It can be a CSV (comma-separated values), TSV (tab-separated values), JSON (javascript object notation) or YAML (yet another markup language) file. +You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It can be a CSV, TSV, JSON or YAML file. ```bash --input '[path to samplesheet file]' ``` -The pipeline supports two types of samplesheets to be used as input: [`fastq`](#fastq-samplesheet) and [`flowcell`](#flowcell-samplesheet) samplesheets. The type will be automatically detected and applied by the pipeline. The pipeline will also auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire. +The pipeline supports two types of samplesheets to be used as input: [`fastq`](#fastq-samplesheet) and [`flowcell`](#flowcell-samplesheet) samplesheets. The type will be automatically detected and applied by the pipeline. FASTQ rows need `fastq_1`; `fastq_2` is optional for single-end data. After demultiplexing, single-end FASTQs are handled if only one read file is produced. ### Fastq samplesheet @@ -31,8 +29,7 @@ A `fastq` samplesheet file consisting of paired-end data may look something like trim_tail: 0 adapter_R1: AGATCGGAAGAGCACACGTCTGAACTCCTTA adapter_R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - run_coverage: true - disable_picard_metrics: false + qc_mode: basic roi: null tag: WES sample_type: DNA @@ -42,28 +39,34 @@ A `fastq` samplesheet file consisting of paired-end data may look something like Following table shows the fields that are used by the `fastq` samplesheet: -| Column | Description | Required | -| ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------- | -| `id` | Unique sample identifier | :heavy_check_mark: | -| `samplename` | The sample name corresponding to the sample in the Fastq file(s) | :heavy_check_mark: | -| `genome` | The genome build to use for the analysis. Currently supports `GRCh38`, `GRCm39` and `GRCz11` | :heavy_check_mark: (unless `organism` is given) | -| `organism` | Full name of the organism. Currently supports `Homo sapiens`, `Mus musculus` and `Danio rerio` | :heavy_check_mark: (unless `genome` is given) | -| `library` | Sample library name | :x: | -| `tag` | The tag used by the sample. Can be one of `WES`, `WGS`, `SeqCap` and `coPGT-M` | :x: | -| `aligner` | The aligner to use for this sample. Can be one of these: `bowtie2`, `bwamem`, `bwamem2`, `dragmap`, `strobe` and `snap`. Set to `false` to output fastq. | :heavy_check_mark: | -| `markdup` | Markdup algorithm to use for duplicate marking. Can be set to `bamsormadup`, `samtools` or `false` | :x: | -| `umi_aware` | Whether UMI-aware processing should be used. Only applies when `markdup` is set to `samtools` | :x: | -| `skip_trimming` | Skip adapter trimming step | :x: | -| `trim_front` | Number of bases to trim from the front of reads | :x: | -| `trim_tail` | Number of bases to trim from the tail of reads | :x: | -| `adapter_R1` | Adapter sequence for read 1 | :x: | -| `adapter_R2` | Adapter sequence for read 2 | :x: | -| `run_coverage` | Run coverage analysis | :x: | -| `disable_picard_metrics` | Disable Picard metrics collection | :x: | -| `roi` | The path to a BED file containing Regions Of Interest for coverage analysis | :x: | -| `sample_type` | Sample type (e.g., `DNA`, `RNA`) | :x: | -| `fastq_1` | FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' | :heavy_check_mark: | -| `fastq_2` | FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' | :x: | +| Column | Description | Required | +| ------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------- | +| `id` | Unique sample identifier | :heavy_check_mark: | +| `samplename` | The sample name corresponding to the sample in the Fastq file(s) | :heavy_check_mark: | +| `genome` | Genome build. Allowed values: `GRCh38`, `GRCh38-noalt`, `GRCm39`, `GRCz11`, `hg38`, `hg38-noalt`. See [organism to genome mapping](#organism-to-genome-mapping) for what is used when only `organism` is set. | :heavy_check_mark: (unless `organism` is given) | +| `organism` | Full name of the organism. Currently supports `Homo sapiens`, `Mus musculus`, `Danio rerio` and `Equus caballus` | :heavy_check_mark: (unless `genome` is given) | +| `library` | Sample library name. When set, results are published under `library/samplename`. | :x: | +| `sequencing_center` | Sequencing centre written to BAM `@RG CN`. | :x: | +| `tag` | Sample tag (`[A-Za-z0-9_-]+`). `SeqCap` restricts panel coverage gene lists to files whose names contain `seqcap`. | :x: | +| `aligner` | DNA aligner: `bowtie2`, `bwamem`, `bwamem2`, `dragmap`, `strobe` or `snap`. Set to `false` to skip alignment and emit FASTQ. RNA samples (`sample_type: RNA`) always use `star`. | :heavy_check_mark: | +| `markdup` | Markdup algorithm to use for duplicate marking. Can be set to `bamsormadup`, `samtools` or `false` | :x: | +| `umi_aware` | Whether UMI-aware processing should be used. Only applies when `markdup` is set to `samtools` | :x: | +| `call_consensus` | Perform consensus calling using the `fgumi` toolsuite. This only works for DNA samples and will always run the SNAP aligner | :x: | +| `fgumi_extract_mode` | UMI extraction mode for fgumi consensus. Use `read_structures` for sequence-based extraction or `read_names` (default) for FASTQ read-name extraction | :x: | +| `fgumi_read_structure_r1` | Read structure for FASTQ read 1 when fgumi_extract_mode is 'read_structures'. | :x: | +| `fgumi_read_structure_r2` | Read structure for FASTQ read 2 when fgumi_extract_mode is 'read_structures'. | :x: | +| `fgumi_simplex_min_reads` | Minimum number of reads required per UMI family for fgumi simplex consensus generation. Defaults to `1` and should be `1` or higher. | :x: | +| `fgumi_snap_ignore_mismatched_pairs` | Pass -I to SNAP to ignore mismatched read IDs in paired-end input when using the `fgumi` toolsuite (`call_consensus` set as `true`). Defaults to `true` | :x: | +| `skip_trimming` | Skip adapter trimming step | :x: | +| `trim_front` | Number of bases to trim from the front of reads | :x: | +| `trim_tail` | Number of bases to trim from the tail of reads | :x: | +| `adapter_R1` | Adapter sequence for read 1 | :x: | +| `adapter_R2` | Adapter sequence for read 2 | :x: | +| `qc_mode` | QC mode for the sample. Can be set to `basic` or `full`. Basic QC includes samtools flagstat, idxstats and mosdepth. Full QC includes samtools stats, samtools coverage, riker metrics and panel coverage in addition to basic QC. | :x: | +| `roi` | The path to a BED file containing Regions Of Interest for coverage analysis | :x: | +| `sample_type` | Sample type. Allowed values: `DNA`, `RNA`, `Tissue`. Defaults to `DNA`. RNA samples are aligned with STAR. | :x: | +| `fastq_1` | FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' | :heavy_check_mark: | +| `fastq_2` | FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'. Omit for single-end data. | :x: | An [example samplesheet](../tests/inputs/test.yml) has been provided with the pipeline. @@ -81,39 +84,57 @@ A `flowcell` samplesheet file consisting of one sequencing run may look somethin Following table shows the fields that are used by the `flowcell` samplesheet: -| Column | Description | Required | -| ------------- | ----------------------------------------------------------------------------------------------------------- | ------------------ | -| `samplesheet` | Illumina flowcell for the flowcell lane | :heavy_check_mark: | -| `sample_info` | JSON/YML file with sample information. See the [flowcell sample info](#flowcell-sample-info) documentation. | :heavy_check_mark: | -| `flowcell` | Illumina flowcell directory | :heavy_check_mark: | -| `lane` | Lane number | :x: | +| Column | Description | Required | +| ------------- | ------------------------------------------------------------------------------------------------------------ | ------------------ | +| `id` | Unique flowcell identifier | :heavy_check_mark: | +| `samplesheet` | Illumina sample sheet CSV for the flowcell lane | :heavy_check_mark: | +| `sample_info` | JSON/YAML file with sample information. See the [flowcell sample info](#flowcell-sample-info) documentation. | :heavy_check_mark: | +| `flowcell` | Illumina flowcell directory | :heavy_check_mark: | +| `lane` | Lane number | :x: | An [example samplesheet](../tests/inputs/test.yml) has been provided with the pipeline. ### Flowcell sample info -A `flowcell` sample info JSON/YML file consisting for one sequencing run may look something like the one below. +A `flowcell` sample info JSON/YAML file for one sequencing run may look something like the one below. ```yml -- id: DNA1_L001 - samplename: DNA_paired1 +- samplename: DNA_paired1 library: test_library genome: GRCh38 aligner: bwamem markdup: bamsormadup umi_aware: false + call_consensus: true + fgumi_extract_mode: read_names skip_trimming: false trim_front: 0 trim_tail: 0 adapter_R1: AGATCGGAAGAGCACACGTCTGAACTCCTTA adapter_R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - run_coverage: true - disable_picard_metrics: false + qc_mode: basic roi: null tag: WES sample_type: DNA ``` +Each row needs `samplename`, `aligner`, `tag`, and either `genome` or `organism`. Analysis fields match the [fastq samplesheet](#fastq-samplesheet). Extra sample-info fields are `purpose` (`research` or `diagnostic`), `vivar_project`, `binsize`, `panels`, and `sequencing_center`. + +The same `samplename` may appear in more than one library. In that case each row needs a distinct `library` value, and the Illumina sample sheet must set `LibraryName` so that BCL Convert `RGLB` matches `sampleinfo.library`. A single row per `samplename` does not need `RGLB` on the demultiplexed FASTQ. + +### Organism to genome mapping + +When a row sets `organism` but no `genome`, the pipeline derives the genome build: + +| Organism | Genome build | +| ---------------- | ------------ | +| `Homo sapiens` | `GRCh38` | +| `Mus musculus` | `mm10` | +| `Danio rerio` | `GRCz11` | +| `Equus caballus` | `EquCab2` | + +Matching is case-insensitive and also accepts an underscore instead of a space. Any other organism leaves the genome unset. Samples whose genome has no entry in `conf/igenomes.config` skip alignment and are QC'd with falco. + ## Running the pipeline The typical command for running the pipeline is as follows: @@ -189,9 +210,9 @@ These options are part of Nextflow and use a _single_ hyphen (pipeline parameter Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Apple containers) - see below. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline loads institutional configs from [nf-core/configs](https://github.com/nf-core/configs) by default (`params.custom_config_base`). If `custom_config_base` points at an nf-cmgg configs tree, it also loads `pipeline/preprocessing.config` from that repo. Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. @@ -204,9 +225,13 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic profile with settings to run the pipeline on ARM64 architecture machines (eg. Apple Silicon). It will use software containers built for ARM64 where available. - `emulate_amd64` - A generic profile with settings to run the pipeline on ARM64 architecture machines (eg. Apple Silicon) using AMD64 software containers. This is for when ARM64 containers are not available but you still want to run the pipeline on an ARM64 machine. Note that this will be slower than using ARM64 containers. +- `apple` + - A generic configuration profile to be used with [Apple containers](https://github.com/apple/container) - `test` - A profile with a complete configuration for automated testing - Includes links to test data so needs no other parameters +- `test_full` + - A profile with a more complete test dataset - `docker` - A generic configuration profile to be used with [Docker](https://docker.com/) - `singularity` @@ -219,6 +244,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) +- `wave` + - Enable Seqera Wave to resolve containers +- `gpu` + - Pass GPU flags through to Docker, Apptainer or Singularity ### `-resume` @@ -250,14 +279,12 @@ A pipeline might not always support every possible argument or option of a parti To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. -### nf-core/configs and nf-cmgg/configs +### Institutional configs -In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-cmgg pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. +Override `custom_config_base` (and usually `custom_config_version`) to use [nf-cmgg/configs](https://github.com/nf-cmgg/configs) instead of the default nf-core configs. Test a one-off config with `-c` first. See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files. -If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. @@ -270,7 +297,7 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted to ## Nextflow memory requirements In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. -We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`): +We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~/.bash_profile`): ```bash NXF_OPTS='-Xms1g -Xmx4g' diff --git a/main.nf b/main.nf index 8d7667e2..c87fe987 100644 --- a/main.nf +++ b/main.nf @@ -16,6 +16,7 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_preprocessing_pipeline' include { PREPROCESSING } from './workflows/preprocessing' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_preprocessing_pipeline' +include { samplePublishDir } from './subworkflows/local/utils_nfcmgg_preprocessing_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW @@ -28,7 +29,7 @@ params { input: Path // The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. - outdir: Path + outdir: String // Email address for completion summary. email: String? @@ -39,16 +40,16 @@ params { genomes: Map = [:] // Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all. - split_fastq: Integer = 100000000 + split_fastq: Integer = 0 // Directory containing gene list bed files for granular coverage analysis genelists: Path? // Git commit id for Institutional configs. - custom_config_version: String = 'main' + custom_config_version: String = 'master' - // Base directory for custom configs. - custom_config_base: String = 'https://raw.githubusercontent.com/nf-cmgg/configs/main' + // Base directory for Institutional configs. + custom_config_base: String = 'https://raw.githubusercontent.com/nf-core/configs/master' // Institutional config name. config_profile_name: String? @@ -80,9 +81,6 @@ params { // Do not use coloured log outputs. monochrome_logs: Boolean = false - // Incoming hook URL for messaging service - hook_url: String = System.getenv('HOOK_URL') - // Custom config file to supply to MultiQC. multiqc_config: Path? @@ -111,13 +109,7 @@ params { show_hidden: Boolean = false // Directory / URL base for iGenomes references. - igenomes_base: String = '/references/' - - // Do not load the iGenomes reference config. - igenomes_ignore: Boolean = false - - // Name of iGenomes reference. - genome: String? + igenomes_base: String = '/references' } workflow { @@ -129,6 +121,7 @@ workflow { PIPELINE_INITIALISATION( params.version, params.validate_params, + params.monochrome_logs, args, params.outdir, params.input, @@ -148,8 +141,8 @@ workflow { ? [file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), params.multiqc_config] : [file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)], params.multiqc_logo ? params.multiqc_logo : [], - params.multiqc_methods_description ? params.multiqc_methods_description : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true), - params.outdir + params.multiqc_methods_description, + params.outdir, ) // @@ -165,47 +158,64 @@ workflow { ) publish: - demultiplex_reports = PREPROCESSING.out.demultiplex_reports.transpose() - demultiplex_logs = PREPROCESSING.out.demultiplex_logs.transpose() - demultiplex_interop = PREPROCESSING.out.demultiplex_interop.transpose(by: 1) - fastq = PREPROCESSING.out.fastq.transpose() - falco_html = PREPROCESSING.out.falco_html.transpose() - falco_txt = PREPROCESSING.out.falco_txt.transpose() - fastp_json = PREPROCESSING.out.fastp_json - fastp_html = PREPROCESSING.out.fastp_html - crams = PREPROCESSING.out.crams - rna_splice_junctions = PREPROCESSING.out.rna_splice_junctions - rna_junctions = PREPROCESSING.out.rna_junctions - align_reports = PREPROCESSING.out.align_reports - sormadup_metrics = PREPROCESSING.out.sormadup_metrics - mosdepth_global = PREPROCESSING.out.mosdepth_global - mosdepth_summary = PREPROCESSING.out.mosdepth_summary - mosdepth_regions = PREPROCESSING.out.mosdepth_regions - mosdepth_per_base_d4 = PREPROCESSING.out.mosdepth_per_base_d4 - mosdepth_per_base_bed = PREPROCESSING.out.mosdepth_per_base_bed - mosdepth_per_base_csi = PREPROCESSING.out.mosdepth_per_base_csi - mosdepth_regions_bed = PREPROCESSING.out.mosdepth_regions_bed - mosdepth_regions_csi = PREPROCESSING.out.mosdepth_regions_csi - mosdepth_quantized_bed = PREPROCESSING.out.mosdepth_quantized_bed - mosdepth_quantized_csi = PREPROCESSING.out.mosdepth_quantized_csi - mosdepth_thresholds_bed = PREPROCESSING.out.mosdepth_thresholds_bed - mosdepth_thresholds_csi = PREPROCESSING.out.mosdepth_thresholds_csi - samtools_coverage = PREPROCESSING.out.samtools_coverage - panelcoverage = PREPROCESSING.out.panelcoverage - samtools_stats = PREPROCESSING.out.samtools_stats - samtools_flagstat = PREPROCESSING.out.samtools_flagstat - samtools_idxstats = PREPROCESSING.out.samtools_idxstats - picard_multiplemetrics = PREPROCESSING.out.picard_multiplemetrics - picard_multiplemetrics_pdf = PREPROCESSING.out.picard_multiplemetrics_pdf - picard_wgsmetrics = PREPROCESSING.out.picard_wgsmetrics - picard_hsmetrics = PREPROCESSING.out.picard_hsmetrics - md5sums = PREPROCESSING.out.md5sums - multiqc_report = PREPROCESSING.out.multiqc_report - multiqc_data = PREPROCESSING.out.multiqc_data - multiqc_plots = PREPROCESSING.out.multiqc_plots - multiqcsav_report = PREPROCESSING.out.multiqcsav_report - multiqcsav_data = PREPROCESSING.out.multiqcsav_data - multiqcsav_plots = PREPROCESSING.out.multiqcsav_plots + demultiplex_reports = PREPROCESSING.out.demultiplex_reports.transpose() + demultiplex_logs = PREPROCESSING.out.demultiplex_logs.transpose() + demultiplex_interop = PREPROCESSING.out.demultiplex_interop.transpose(by: 1) + fastq = PREPROCESSING.out.fastq.transpose() + falco_html = PREPROCESSING.out.falco_html.transpose() + falco_txt = PREPROCESSING.out.falco_txt.transpose() + fastp_json = PREPROCESSING.out.fastp_json + fastp_html = PREPROCESSING.out.fastp_html + crams = PREPROCESSING.out.crams + rna_splice_junctions = PREPROCESSING.out.rna_splice_junctions + rna_junctions = PREPROCESSING.out.rna_junctions + align_reports = PREPROCESSING.out.align_reports + sormadup_metrics = PREPROCESSING.out.sormadup_metrics + mosdepth_global = PREPROCESSING.out.mosdepth_global + mosdepth_summary = PREPROCESSING.out.mosdepth_summary + mosdepth_regions = PREPROCESSING.out.mosdepth_regions + mosdepth_per_base_d4 = PREPROCESSING.out.mosdepth_per_base_d4 + mosdepth_per_base_bed = PREPROCESSING.out.mosdepth_per_base_bed + mosdepth_per_base_csi = PREPROCESSING.out.mosdepth_per_base_csi + mosdepth_regions_bed = PREPROCESSING.out.mosdepth_regions_bed + mosdepth_regions_csi = PREPROCESSING.out.mosdepth_regions_csi + mosdepth_quantized_bed = PREPROCESSING.out.mosdepth_quantized_bed + mosdepth_quantized_csi = PREPROCESSING.out.mosdepth_quantized_csi + mosdepth_thresholds_bed = PREPROCESSING.out.mosdepth_thresholds_bed + mosdepth_thresholds_csi = PREPROCESSING.out.mosdepth_thresholds_csi + samtools_coverage = PREPROCESSING.out.samtools_coverage + panelcoverage = PREPROCESSING.out.panelcoverage + samtools_stats = PREPROCESSING.out.samtools_stats + samtools_flagstat = PREPROCESSING.out.samtools_flagstat + samtools_idxstats = PREPROCESSING.out.samtools_idxstats + riker_alignment_metrics = PREPROCESSING.out.riker_alignment_metrics + riker_base_dist = PREPROCESSING.out.riker_base_dist + riker_mean_qual = PREPROCESSING.out.riker_mean_qual + riker_qual_dist = PREPROCESSING.out.riker_qual_dist + riker_error_mismatch = PREPROCESSING.out.riker_error_mismatch + riker_error_overlap = PREPROCESSING.out.riker_error_overlap + riker_error_indel = PREPROCESSING.out.riker_error_indel + riker_gcbias_detail = PREPROCESSING.out.riker_gcbias_detail + riker_gcbias_summary = PREPROCESSING.out.riker_gcbias_summary + riker_hybcap_metrics = PREPROCESSING.out.riker_hybcap_metrics + riker_hybcap_per_target = PREPROCESSING.out.riker_hybcap_per_target + riker_hybcap_per_base = PREPROCESSING.out.riker_hybcap_per_base + riker_isize_metrics = PREPROCESSING.out.riker_isize_metrics + riker_isize_histogram = PREPROCESSING.out.riker_isize_histogram + riker_wgs_metrics = PREPROCESSING.out.riker_wgs_metrics + riker_wgs_coverage = PREPROCESSING.out.riker_wgs_coverage + riker_pdf = PREPROCESSING.out.riker_pdf + riker_rna_biotype = PREPROCESSING.out.riker_rna_biotype + riker_rna_insert_size_histogram = PREPROCESSING.out.riker_rna_insert_size_histogram + riker_rna_insert_size = PREPROCESSING.out.riker_rna_insert_size + riker_rna_metrics = PREPROCESSING.out.riker_rna_metrics + md5sums = PREPROCESSING.out.md5sums + multiqc_report = PREPROCESSING.out.multiqc_report + multiqc_data = PREPROCESSING.out.multiqc_data + multiqc_plots = PREPROCESSING.out.multiqc_plots + multiqcsav_report = PREPROCESSING.out.multiqcsav_report + multiqcsav_data = PREPROCESSING.out.multiqcsav_data + multiqcsav_plots = PREPROCESSING.out.multiqcsav_plots } output { @@ -221,168 +231,253 @@ output { } demultiplex_interop { path { _meta, bin -> - bin >> "Interop/${bin.name}" + bin >> "InterOp/${bin.name}" } } fastq { path { meta, fastq -> - fastq >> (meta.library ? "${meta.library}/${meta.samplename}/${fastq.name}" : "${meta.samplename}/${fastq.name}") + fastq >> "${samplePublishDir(meta)}/${fastq.name}" } } falco_html { path { meta, html -> - html >> (meta.library ? "${meta.library}/${meta.samplename}/${html.name}" : "${meta.samplename}/${html.name}") + html >> "${samplePublishDir(meta)}/${html.name}" } } falco_txt { path { meta, txt -> - txt >> (meta.library ? "${meta.library}/${meta.samplename}/${txt.name}" : "${meta.samplename}/${txt.name}") + txt >> "${samplePublishDir(meta)}/${txt.name}" } } fastp_json { path { meta, json -> - json >> (meta.library ? "${meta.library}/${meta.samplename}/${json.name}" : "${meta.samplename}/${json.name}") + json >> "${samplePublishDir(meta)}/${json.name}" } } fastp_html { path { meta, html -> - html >> (meta.library ? "${meta.library}/${meta.samplename}/${html.name}" : "${meta.samplename}/${html.name}") + html >> "${samplePublishDir(meta)}/${html.name}" } } crams { path { meta, cram, crai -> - cram >> (meta.library ? "${meta.library}/${meta.samplename}/${meta.samplename}.cram" : "${meta.samplename}/${meta.samplename}.cram") - crai >> (meta.library ? "${meta.library}/${meta.samplename}/${meta.samplename}.cram.crai" : "${meta.samplename}/${meta.samplename}.cram.crai") + cram >> "${samplePublishDir(meta)}/${meta.samplename}.cram" + crai >> "${samplePublishDir(meta)}/${meta.samplename}.cram.crai" } } rna_splice_junctions { path { meta, sjt -> - sjt >> (meta.library ? "${meta.library}/${meta.samplename}/${sjt.name}" : "${meta.samplename}/${sjt.name}") + sjt >> "${samplePublishDir(meta)}/${sjt.name}" } } rna_junctions { path { meta, junctions -> - junctions >> (meta.library ? "${meta.library}/${meta.samplename}/${junctions.name}" : "${meta.samplename}/${junctions.name}") + junctions >> "${samplePublishDir(meta)}/${junctions.name}" } } align_reports { path { meta, log -> - log >> (meta.library ? "${meta.library}/${meta.samplename}/${log.name}" : "${meta.samplename}/${log.name}") + log >> "${samplePublishDir(meta)}/${log.name}" } } sormadup_metrics { path { meta, metrics -> - metrics >> (meta.library ? "${meta.library}/${meta.samplename}/${meta.samplename}.duplicate_metrics.txt" : "${meta.samplename}/${meta.samplename}.duplicate_metrics.txt") + metrics >> "${samplePublishDir(meta)}/${meta.samplename}.duplicate_metrics.txt" } } mosdepth_global { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_summary { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_regions { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_per_base_d4 { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_per_base_bed { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_per_base_csi { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_regions_bed { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_regions_csi { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_quantized_bed { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_quantized_csi { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_thresholds_bed { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } mosdepth_thresholds_csi { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } samtools_coverage { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } panelcoverage { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } samtools_stats { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } samtools_flagstat { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } samtools_idxstats { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" + } + } + riker_alignment_metrics { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_base_dist { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_mean_qual { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_qual_dist { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_error_mismatch { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_error_overlap { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_error_indel { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_gcbias_detail { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_gcbias_summary { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_hybcap_metrics { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_hybcap_per_target { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_hybcap_per_base { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_isize_metrics { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_isize_histogram { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_wgs_metrics { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_wgs_coverage { + path { meta, _file -> + return "${samplePublishDir(meta)}/" + } + } + riker_pdf { + path { meta, _file -> + return "${samplePublishDir(meta)}/" } } - picard_multiplemetrics { + riker_rna_biotype { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } - picard_multiplemetrics_pdf { + riker_rna_insert_size_histogram { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } - picard_wgsmetrics { + riker_rna_insert_size { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } - picard_hsmetrics { + riker_rna_metrics { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } md5sums { path { meta, _file -> - return (meta.library ? "${meta.library}/${meta.samplename}/" : "${meta.samplename}/") + return "${samplePublishDir(meta)}/" } } multiqcsav_report { diff --git a/modules.json b/modules.json index 328d7a78..2badde5d 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bclconvert": { "branch": "master", - "git_sha": "21e4662ae927fdbc5fc04eec9bde38b0689d4954", + "git_sha": "8b798ea24b2d639ef4d204add9ddb35dc0d8279f", "installed_by": ["modules"] }, "biobambam/bamsormadup": { @@ -18,7 +18,7 @@ }, "bowtie2/align": { "branch": "master", - "git_sha": "a0961c41021561ac7cf139f86bd7812a2f99e994", + "git_sha": "2080397432fcb0d079121dbacf22ce42ef175cec", "installed_by": ["fastq_align_dna", "modules"], "patch": "modules/nf-core/bowtie2/align/bowtie2-align.diff" }, @@ -30,7 +30,7 @@ }, "bwamem2/mem": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "62ce917fd775aaef732eb82019de069c765adfd3", "installed_by": ["fastq_align_dna"], "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff" }, @@ -47,9 +47,31 @@ }, "fastp": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "826a9b28d6da61097d60e1923bb8a2e51de3c5b4", "installed_by": ["modules"] }, + "fgumi/filter": { + "branch": "master", + "git_sha": "4dd270e412e2a7e78761be38aafa5cfa1dcdf891", + "installed_by": ["modules"], + "patch": "modules/nf-core/fgumi/filter/fgumi-filter.diff" + }, + "fgumi/group": { + "branch": "master", + "git_sha": "4dd270e412e2a7e78761be38aafa5cfa1dcdf891", + "installed_by": ["modules"] + }, + "fgumi/merge": { + "branch": "master", + "git_sha": "9fd3ec2625f849749bc39596f30d0d2a08c49845", + "installed_by": ["modules"] + }, + "fgumi/simplex": { + "branch": "master", + "git_sha": "4dd270e412e2a7e78761be38aafa5cfa1dcdf891", + "installed_by": ["modules"], + "patch": "modules/nf-core/fgumi/simplex/fgumi-simplex.diff" + }, "gnu/sort": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", @@ -68,75 +90,64 @@ }, "multiqc": { "branch": "master", - "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", - "installed_by": ["modules"] + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", + "installed_by": ["modules"], + "patch": "modules/nf-core/multiqc/multiqc.diff" }, "multiqcsav": { "branch": "master", - "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", + "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686", "installed_by": ["modules"] }, - "picard/collecthsmetrics": { - "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["modules"], - "patch": "modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff" - }, - "picard/collectmultiplemetrics": { + "riker/multi": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686", "installed_by": ["modules"], - "patch": "modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff" - }, - "picard/collectwgsmetrics": { - "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["modules"], - "patch": "modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff" + "patch": "modules/nf-core/riker/multi/riker-multi.diff" }, "samtools/convert": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002", "installed_by": ["modules"], "patch": "modules/nf-core/samtools/convert/samtools-convert.diff" }, "samtools/coverage": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002", "installed_by": ["modules"], "patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff" }, "samtools/flagstat": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002", "installed_by": ["modules"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002", "installed_by": ["modules"] }, "samtools/sormadup": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002", "installed_by": ["modules"], "patch": "modules/nf-core/samtools/sormadup/samtools-sormadup.diff" }, "samtools/sort": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002", "installed_by": ["modules"], "patch": "modules/nf-core/samtools/sort/samtools-sort.diff" }, "samtools/stats": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002", "installed_by": ["modules"], "patch": "modules/nf-core/samtools/stats/samtools-stats.diff" }, "snapaligner/align": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "c8ebae73f5cd2886ad8e3e28d52fe6f6f22cd9ca", "installed_by": ["fastq_align_dna", "modules"], "patch": "modules/nf-core/snapaligner/align/snapaligner-align.diff" }, @@ -148,7 +159,7 @@ }, "strobealign": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "4dd270e412e2a7e78761be38aafa5cfa1dcdf891", "installed_by": ["fastq_align_dna", "modules"], "patch": "modules/nf-core/strobealign/strobealign.diff" } @@ -158,23 +169,23 @@ "nf-core": { "fastq_align_dna": { "branch": "master", - "git_sha": "a0961c41021561ac7cf139f86bd7812a2f99e994", + "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686", "installed_by": ["subworkflows"], "patch": "subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff" }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75", + "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", + "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12", + "git_sha": "f6d4527ae18ee2e3276e6965ac64ee798e12d24b", "installed_by": ["subworkflows"] } } diff --git a/modules/local/fgumi/extractsort/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt b/modules/local/fgumi/extractsort/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt new file mode 100644 index 00000000..7e7df88e --- /dev/null +++ b/modules/local/fgumi/extractsort/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt @@ -0,0 +1,1439 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: 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+license_family: BSD +size: 615477 +timestamp: 1786599613561 diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/local/fgumi/extractsort/environment.yml similarity index 68% rename from modules/nf-core/picard/collecthsmetrics/environment.yml rename to modules/local/fgumi/extractsort/environment.yml index b4ac4fe0..c417e292 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/local/fgumi/extractsort/environment.yml @@ -4,5 +4,4 @@ channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/picard - - bioconda::picard=3.4.0 + - "bioconda::fgumi=0.7.0" diff --git a/modules/local/fgumi/extractsort/main.nf b/modules/local/fgumi/extractsort/main.nf new file mode 100644 index 00000000..7478f429 --- /dev/null +++ b/modules/local/fgumi/extractsort/main.nf @@ -0,0 +1,46 @@ +process FGUMI_EXTRACTSORT { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' + : 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a'}" + + input: + tuple val(meta), path(reads), val(library) + + output: + tuple val(meta), path("*.bam"), emit: bam + tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | sed "s/^fgumi //"'), topic: versions, emit: versions_fgumi + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + fgumi extract \\ + --inputs ${reads.join(' ')} \\ + --output - \\ + --sample ${prefix} \\ + --library "${library}" \\ + ${args} \\ + | fgumi sort \\ + --input - \\ + --output ${prefix}.bam \\ + --threads ${task.cpus} \\ + --max-memory ${task.memory.toGiga() / task.cpus}G \\ + --tmp-dir . \\ + ${args2} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + """ +} diff --git a/modules/local/fgumi/extractsort/meta.yml b/modules/local/fgumi/extractsort/meta.yml new file mode 100644 index 00000000..b375b285 --- /dev/null +++ b/modules/local/fgumi/extractsort/meta.yml @@ -0,0 +1,92 @@ +name: fgumi_extract +description: Extract unique molecular indices (UMIs) from FASTQ files and write a sorted unaligned BAM file. +keywords: + - umi + - extract + - fastq + - bam +tools: + - fgumi: + description: High-performance tools for working with UMI-tagged sequencing data. + homepage: https://github.com/fulcrumgenomics/fgumi + documentation: https://docs.rs/fgumi + tool_dev_url: https://github.com/fulcrumgenomics/fgumi + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input FASTQ files used for UMI extraction. + pattern: "*.fastq.gz" + ontologies: + - edam: http://edamontology.org/format_3989 + - library: + type: string + description: Library name to store in the output BAM read group. +output: + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Unaligned BAM with extracted UMIs in SAM tags. + pattern: "*.bam" + ontologies: [] + versions_fgumi: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - 'fgumi --version | sed "s/^fgumi //"': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - 'fgumi --version | sed "s/^fgumi //"': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@atrigila" +maintainers: + - "@atrigila" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb + build_id: bd-595c95b71b3df5bb_1 + scan_id: sc-61ac7030bb5e32a9_1 + linux/amd64: + name: community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a + build_id: bd-d91f99b4cd4aae5a_1 + scan_id: sc-760abd46b15b110e_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55 + build_id: bd-e2a3aedc6034aa55_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data + linux/arm64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b + build_id: bd-72ed3ddc0a890f6b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data + conda: + linux/amd64: + lock_file: modules/nf-core/fgumi/extract/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt + linux/arm64: + lock_file: modules/nf-core/fgumi/extract/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt diff --git a/modules/local/fgumi/extractsort/tests/main.nf.test b/modules/local/fgumi/extractsort/tests/main.nf.test new file mode 100644 index 00000000..cf7bedd5 --- /dev/null +++ b/modules/local/fgumi/extractsort/tests/main.nf.test @@ -0,0 +1,73 @@ +nextflow_process { + + name "Test Process FGUMI_EXTRACTSORT" + script "../main.nf" + process "FGUMI_EXTRACTSORT" + + tag "modules" + tag "modules_nfcore" + tag "fgumi" + tag "fgumi/extractsort" + + config "./nextflow.config" + + test("homo_sapiens - [fastq1, fastq2]") { + + when { + params { + module_args = '--read-structures +T +M' + } + process { + """ + input[0] = [ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true) + ], + 'illumina', + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match() } + ) + } + + } + + test("homo_sapiens - [fastq1, fastq2] - stub") { + + options "-stub" + + when { + params { + module_args = "--read-structures +T +M" + } + process { + """ + input[0] = [ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true) + ], + 'test', + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + + } +} diff --git a/modules/local/fgumi/extractsort/tests/main.nf.test.snap b/modules/local/fgumi/extractsort/tests/main.nf.test.snap new file mode 100644 index 00000000..68f348d4 --- /dev/null +++ b/modules/local/fgumi/extractsort/tests/main.nf.test.snap @@ -0,0 +1,54 @@ +{ + "homo_sapiens - [fastq1, fastq2]": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test.fgumi.unmapped.bam" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_EXTRACTSORT", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-09-16T15:59:25.807775", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - [fastq1, fastq2] - stub": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test.fgumi.unmapped.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_EXTRACTSORT", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-09-16T13:43:37.727741", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/local/fgumi/extractsort/tests/nextflow.config b/modules/local/fgumi/extractsort/tests/nextflow.config new file mode 100644 index 00000000..286a51b0 --- /dev/null +++ b/modules/local/fgumi/extractsort/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: FGUMI_EXTRACTSORT { + ext.args = { "${params.module_args}" } + } +} diff --git a/modules/local/fgumi/snapzipsort/environment.yml b/modules/local/fgumi/snapzipsort/environment.yml new file mode 100644 index 00000000..7b05692a --- /dev/null +++ b/modules/local/fgumi/snapzipsort/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/fgumi + - bioconda::fgumi=0.7.0 + # renovate: datasource=conda depName=bioconda/snap-aligner + - bioconda::snap-aligner=2.0.5 diff --git a/modules/local/fgumi/snapzipsort/main.nf b/modules/local/fgumi/snapzipsort/main.nf new file mode 100644 index 00000000..333e4ebe --- /dev/null +++ b/modules/local/fgumi/snapzipsort/main.nf @@ -0,0 +1,69 @@ +process FGUMI_SNAPZIPSORT { + tag "${meta.id}" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fa/fa173043be444ca10a7b50fb74d46b643c75abd24547fbfeae8dd75af9172b63/data' + : 'community.wave.seqera.io/library/fgumi_snap-aligner:cafdcb9148178d5f'}" + + input: + tuple val(meta), path(unmapped_bam), path(index, stageAs: "index/*"), path(fasta), path(fai), path(dict) + + output: + tuple val(meta), path("${prefix}.bam"), emit: bam + tuple val(meta), path("${prefix}.bam.bai"), emit: bai, optional: true + tuple val("${task.process}"), val('fgumi'), eval("fgumi --version | sed 's/^fgumi //;q'"), topic: versions + tuple val("${task.process}"), val('snap-aligner'), eval("snap-aligner 2>&1 | sed 's/^.*version //;s/.\$//;q'"), topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' + def args4 = task.ext.args4 ?: '' + prefix = task.ext.prefix ?: "${meta.id}.fgumi" + + """ + # SNAP index directory is resolved from staged index content. + INDEX_FILE=\$(find -L ./ -name "OverflowTable*" -print -quit) + [ -z "\$INDEX_FILE" ] && echo "Snap index files not found" 1>&2 && exit 1 + INDEX=\$(dirname "\$INDEX_FILE") + + snap-aligner paired \\ + \$INDEX \\ + ${unmapped_bam} \\ + -t ${task.cpus} \\ + -o -bam - \\ + ${args} \\ + | fgumi sort \\ + --input - \\ + --output - \\ + --threads ${task.cpus} \\ + --max-memory ${task.memory.toGiga() / task.cpus}G \\ + --tmp-dir ./tmp_sort1 \\ + ${args2} \\ + | fgumi zipper \\ + --input - \\ + --output - \\ + --unmapped ${unmapped_bam} \\ + --reference ${fasta} \\ + --threads ${task.cpus} \\ + ${args3} \\ + | fgumi sort \\ + --input - \\ + --output ${prefix}.bam \\ + --threads ${task.cpus} \\ + --max-memory ${task.memory.toGiga() / task.cpus}G \\ + --tmp-dir ./tmp_sort2 \\ + ${args4} + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}.fgumi" + """ + touch ${prefix}.bam + """ +} diff --git a/modules/local/fgumi/snapzipsort/tests/main.nf.test b/modules/local/fgumi/snapzipsort/tests/main.nf.test new file mode 100644 index 00000000..4a7a47c6 --- /dev/null +++ b/modules/local/fgumi/snapzipsort/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process FGUMI_SNAPZIPSORT" + script "modules/local/fgumi/snapzipsort/main.nf" + process "FGUMI_SNAPZIPSORT" + config "./nextflow.config" + + tag "modules" + tag "modules/local" + tag "modules/local/fgumi/snapzipsort" + + topics "versions" + + test("homo sapiens - test") { + + when { + process { + """ + input[0] = [ + [id: "test", single_end: false ], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/bams/umi.unmapped.bam", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/snap/", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists:true) + ] + """ + } + } + then { + assert process.success + assert snapshot(sanitizeOutput(process.out, unstableKeys:["bam","bai"]), topics).match() + } + + } + + test("homo sapiens - test - stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [id: "test", single_end: false ], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/bams/umi.unmapped.bam", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/snap/", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists:true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists:true) + ] + """ + } + } + then { + assert process.success + assert snapshot(sanitizeOutput(process.out), topics).match() + } + } + +} diff --git a/modules/local/fgumi/snapzipsort/tests/main.nf.test.snap b/modules/local/fgumi/snapzipsort/tests/main.nf.test.snap new file mode 100644 index 00000000..395962e7 --- /dev/null +++ b/modules/local/fgumi/snapzipsort/tests/main.nf.test.snap @@ -0,0 +1,76 @@ +{ + "homo sapiens - test": { + "content": [ + { + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fgumi.bam" + ] + ] + }, + { + "versions": [ + [ + "FGUMI_SNAPZIPSORT", + "fgumi", + "0.7.0" + ], + [ + "FGUMI_SNAPZIPSORT", + "snap-aligner", + "2.0.5" + ] + ] + } + ], + "timestamp": "2026-09-08T11:56:58.495522", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo sapiens - test - stub": { + "content": [ + { + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fgumi.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + }, + { + "versions": [ + [ + "FGUMI_SNAPZIPSORT", + "fgumi", + "0.7.0" + ], + [ + "FGUMI_SNAPZIPSORT", + "snap-aligner", + "2.0.5" + ] + ] + } + ], + "timestamp": "2026-09-08T12:01:16.811993", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/local/fgumi/snapzipsort/tests/nextflow.config b/modules/local/fgumi/snapzipsort/tests/nextflow.config new file mode 100644 index 00000000..247553f3 --- /dev/null +++ b/modules/local/fgumi/snapzipsort/tests/nextflow.config @@ -0,0 +1,21 @@ +process { + withName: FGUMI_SNAPZIPSORT { + // SNAP + ext.args = "" + // Initial Sort + ext.args2 = { + ["--order queryname::natural", "--compression-level 0", "--key-types mi"].join(" ").trim() + } + // Zipper + ext.args3 = { + ["--compression-level 0"].join(" ").trim() + } + // Final Sort + ext.args4 = { + [ + "--order template-coordinate", + "--key-types mi", + ].join(" ").trim() + } + } +} diff --git a/tests/modules/local/panelcoverage/main.nf.test b/modules/local/panelcoverage/tests/main.nf.test similarity index 93% rename from tests/modules/local/panelcoverage/main.nf.test rename to modules/local/panelcoverage/tests/main.nf.test index 4a2dd77d..e8c41bb4 100644 --- a/tests/modules/local/panelcoverage/main.nf.test +++ b/modules/local/panelcoverage/tests/main.nf.test @@ -27,7 +27,7 @@ nextflow_process { then { assert process.success - assert snapshot(process.out).match() + assert snapshot(sanitizeOutput(process.out), topics).match() } } diff --git a/tests/modules/local/panelcoverage/main.nf.test.snap b/modules/local/panelcoverage/tests/main.nf.test.snap similarity index 51% rename from tests/modules/local/panelcoverage/main.nf.test.snap rename to modules/local/panelcoverage/tests/main.nf.test.snap index 49122c84..df1e76ab 100644 --- a/tests/modules/local/panelcoverage/main.nf.test.snap +++ b/modules/local/panelcoverage/tests/main.nf.test.snap @@ -2,29 +2,6 @@ "test": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_genelist_chr21_per_exon.mosdepth.region.dist.txt:md5,b29a7f12cef3be13215923edf6dde674" - ] - ], - "1": [ - [ - "PANELCOVERAGE", - "cmgg_genelists", - "0.1.0" - ] - ], - "2": [ - [ - "PANELCOVERAGE", - "bedtools", - "2.31.1" - ] - ], "regiondist": [ [ { @@ -48,12 +25,15 @@ "0.1.0" ] ] + }, + { + } ], - "timestamp": "2026-02-11T19:45:02.994288", + "timestamp": "2026-09-08T11:33:14.358385", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/modules/nf-core/bclconvert/Dockerfile b/modules/nf-core/bclconvert/Dockerfile index c5594cf2..11ceb323 100644 --- a/modules/nf-core/bclconvert/Dockerfile +++ b/modules/nf-core/bclconvert/Dockerfile @@ -4,7 +4,7 @@ # Build stage: unpack the RPM file FROM debian:bullseye-slim AS build -ARG BCLCONVERT_VERSION="4.4.6" +ARG BCLCONVERT_VERSION="4.5.4" # Install tools needed to extract RPM RUN apt-get update \ @@ -15,13 +15,13 @@ RUN apt-get update \ && rm -rf /var/lib/apt/lists/* # Extract bcl-convert from RPM -COPY bcl-convert-4.4.6-2.el8.x86_64.rpm bcl-convert.rpm +COPY bcl-convert-${BCLCONVERT_VERSION}-2.el8.x86_64.rpm bcl-convert.rpm RUN rpm2cpio bcl-convert.rpm | cpio -idmv \ && rm bcl-convert.rpm # Final stage: minimal image with only necessary components FROM debian:bullseye-slim -ARG BCLCONVERT_VERSION="4.4.6" +ARG BCLCONVERT_VERSION="4.5.4" LABEL org.opencontainers.image.description="Docker image containing bcl-convert" LABEL org.opencontainers.image.version="$BCLCONVERT_VERSION" LABEL org.opencontainers.image.documentation="https://github.com/nf-core/modules/blob/master/modules/nf-core/bclconvert/README.md" diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf index 6b32e54e..413c3014 100644 --- a/modules/nf-core/bclconvert/main.nf +++ b/modules/nf-core/bclconvert/main.nf @@ -2,7 +2,7 @@ process BCLCONVERT { tag "${ meta.lane ? meta.id + "." + meta.lane : meta.id }" label 'process_high' - container "quay.io/nf-core/bclconvert:4.4.6" + container "quay.io/nf-core/bclconvert:4.5.4" input: tuple val(meta), path(samplesheet), path(run_dir) @@ -70,8 +70,8 @@ process BCLCONVERT { stub: """ mkdir -p output - echo "fake fastq file" | gzip > output/Sample1_S1_L001_R1_001.fastq.gz - echo "fake fastq file" | gzip > output/Undetermined_S0_L001_R1_001.fastq.gz + echo "" | gzip > output/Sample1_S1_L001_R1_001.fastq.gz + echo "" | gzip > output/Undetermined_S0_L001_R1_001.fastq.gz mkdir -p output/Reports echo "fake report file" > output/Reports/Adapter_Cycle_Metrics.csv diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap index b228a5b2..2d03f38b 100644 --- a/modules/nf-core/bclconvert/tests/main.nf.test.snap +++ b/modules/nf-core/bclconvert/tests/main.nf.test.snap @@ -49,16 +49,16 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ] } ], + "timestamp": "2026-05-22T13:52:39.325893", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-04T20:03:26.54479" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } }, "homo_sapiens illumina [bcl] - stub": { "content": [ @@ -69,7 +69,7 @@ "id": "test", "lane": 1 }, - "Sample1_S1_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Sample1_S1_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -81,7 +81,7 @@ "id": "test", "lane": 1 }, - "Undetermined_S0_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Undetermined_S0_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "3": [ @@ -144,7 +144,7 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ], "fastq": [ @@ -153,7 +153,7 @@ "id": "test", "lane": 1 }, - "Sample1_S1_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Sample1_S1_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "fastq_idx": [ @@ -218,7 +218,7 @@ "id": "test", "lane": 1 }, - "Undetermined_S0_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Undetermined_S0_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "undetermined_idx": [ @@ -228,16 +228,16 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ] } ], + "timestamp": "2026-05-27T10:04:20.149645", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-02-17T14:13:11.717962" + "nf-test": "0.9.5", + "nextflow": "26.04.2" + } }, "homo_sapiens illumina [bcl]": { "content": [ @@ -281,15 +281,15 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ] } ], + "timestamp": "2026-05-22T13:52:14.995144", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-04T20:02:51.80369" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } } } \ No newline at end of file diff --git a/modules/nf-core/bowtie2/align/bowtie2-align.diff b/modules/nf-core/bowtie2/align/bowtie2-align.diff index 33d3a5cf..20c0e003 100644 --- a/modules/nf-core/bowtie2/align/bowtie2-align.diff +++ b/modules/nf-core/bowtie2/align/bowtie2-align.diff @@ -17,6 +17,7 @@ Changes in 'bowtie2/align/main.nf': 'modules/nf-core/bowtie2/align/tests/main.nf.test.snap' is unchanged +'modules/nf-core/bowtie2/align/tests/bam.config' is unchanged 'modules/nf-core/bowtie2/align/tests/large_index.config' is unchanged 'modules/nf-core/bowtie2/align/tests/sam2.config' is unchanged 'modules/nf-core/bowtie2/align/tests/main.nf.test' is unchanged diff --git a/modules/nf-core/bowtie2/align/tests/bam.config b/modules/nf-core/bowtie2/align/tests/bam.config new file mode 100644 index 00000000..78caeaff --- /dev/null +++ b/modules/nf-core/bowtie2/align/tests/bam.config @@ -0,0 +1,8 @@ +process { + withName: BOWTIE2_BUILD { + ext.args = '--seed 1' + } + withName: BOWTIE2_ALIGN { + ext.args = '--seed 1' + } +} diff --git a/modules/nf-core/bowtie2/align/tests/large_index.config b/modules/nf-core/bowtie2/align/tests/large_index.config index b2f0c405..c9cb76ed 100644 --- a/modules/nf-core/bowtie2/align/tests/large_index.config +++ b/modules/nf-core/bowtie2/align/tests/large_index.config @@ -1,5 +1,8 @@ process { withName: BOWTIE2_BUILD { - ext.args = '--large-index' + ext.args = '--large-index --seed 1' + } + withName: BOWTIE2_ALIGN { + ext.args = '--seed 1' } } diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test index 214c97cc..6777e4f4 100644 --- a/modules/nf-core/bowtie2/align/tests/main.nf.test +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test @@ -9,8 +9,9 @@ nextflow_process { tag "bowtie2/build" tag "bowtie2/align" - test("sarscov2 - fastq, index, fasta_fai, false, false - bam") { + test("sarscov2 - fastq, index, fasta_fai, false, true - bam") { + config "./bam.config" setup { run("BOWTIE2_BUILD") { script "../../build/main.nf" @@ -47,7 +48,11 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), + // Conda and docker version of bowtie2 produce different + // hashes. Therefore, testing whether file exists and bam + // statistics. + file(process.out.bam[0][1]).name, + bam(process.out.bam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } @@ -57,7 +62,7 @@ nextflow_process { } - test("sarscov2 - fastq, index, fasta_fai, false, false - sam") { + test("sarscov2 - fastq, index, fasta_fai, false, true - sam") { config "./sam.config" setup { @@ -96,7 +101,8 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.sam[0][1]).getSamLines(5), + file(process.out.sam[0][1]).name, + bam(process.out.sam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } @@ -106,7 +112,7 @@ nextflow_process { } - test("sarscov2 - fastq, index, fasta_fai, false, false - sam2") { + test("sarscov2 - fastq, index, fasta_fai, false, true - sam2") { config "./sam2.config" setup { @@ -145,7 +151,8 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.sam[0][1]).getSamLines(5), + file(process.out.sam[0][1]).name, + bam(process.out.sam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } @@ -155,8 +162,9 @@ nextflow_process { } - test("sarscov2 - fastq, index, fasta_fai, false, true - bam") { + test("sarscov2 - fastq, index, fasta_fai, true, true - bam") { + config "./bam.config" setup { run("BOWTIE2_BUILD") { script "../../build/main.nf" @@ -183,7 +191,7 @@ nextflow_process { [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[3] = false //save_unaligned + input[3] = true //save_unaligned input[4] = true //sort """ } @@ -193,7 +201,11 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), + // Conda and docker version of bowtie2 produce different + // hashes. Therefore, testing whether file exists and bam + // statistics. + file(process.out.bam[0][1]).name, + bam(process.out.bam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } @@ -203,8 +215,9 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], index, fasta_fai, false, false - bam") { + test("sarscov2 - [fastq1, fastq2], index, fasta_fai, false, true - bam") { + config "./bam.config" setup { run("BOWTIE2_BUILD") { script "../../build/main.nf" @@ -244,7 +257,11 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), + // Conda and docker version of bowtie2 produce different + // hashes. Therefore, testing whether file exists and bam + // statistics. + file(process.out.bam[0][1]).name, + bam(process.out.bam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } @@ -254,8 +271,9 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], index, fasta_fai, false, true - bam") { + test("sarscov2 - [fastq1, fastq2], index, fasta_fai, true, true - bam") { + config "./bam.config" setup { run("BOWTIE2_BUILD") { script "../../build/main.nf" @@ -285,7 +303,7 @@ nextflow_process { [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[3] = false //save_unaligned + input[3] = true //save_unaligned input[4] = true //sort """ } @@ -295,7 +313,11 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), + // Conda and docker version of bowtie2 produce different + // hashes. Therefore, testing whether file exists and bam + // statistics. + file(process.out.bam[0][1]).name, + bam(process.out.bam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } @@ -305,7 +327,7 @@ nextflow_process { } - test("sarscov2 - fastq, large_index, fasta_fai, false, false - bam") { + test("sarscov2 - fastq, large_index, fasta_fai, false, true - bam") { config "./large_index.config" setup { @@ -344,7 +366,11 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), + // Conda and docker version of bowtie2 produce different + // hashes. Therefore, testing whether file exists and bam + // statistics. + file(process.out.bam[0][1]).name, + bam(process.out.bam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } @@ -354,7 +380,7 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], large_index, fasta_fai, false, false - bam") { + test("sarscov2 - [fastq1, fastq2], large_index, fasta_fai, false, true - bam") { config "./large_index.config" setup { @@ -396,117 +422,21 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), - process.out.log, - process.out.fastq, - process.out.findAll { key, val -> key.startsWith('versions') } - ).match() } - ) - } - - } - - test("sarscov2 - [fastq1, fastq2], index, fasta_fai, true, false - bam") { - - setup { - run("BOWTIE2_BUILD") { - script "../../build/main.nf" - process { - """ - input[0] = [ - [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - """ - } - } - } - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) - ] - ] - input[1] = BOWTIE2_BUILD.out.index - input[2] = [ - [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[3] = false //save_unaligned - input[4] = true //sort - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), - process.out.log, - process.out.fastq, - process.out.findAll { key, val -> key.startsWith('versions') } - ).match() } - ) - } - - } - - test("sarscov2 - fastq, index, fasta_fai, true, false - bam") { - - setup { - run("BOWTIE2_BUILD") { - script "../../build/main.nf" - process { - """ - input[0] = [ - [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - """ - } - } - } - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ] - input[1] = BOWTIE2_BUILD.out.index - input[2] = [ - [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[3] = false //save_unaligned - input[4] = true //sort - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot( - bam(process.out.bam[0][1]).getSamLines(5), + // Conda and docker version of bowtie2 produce different + // hashes. Therefore, testing whether file exists and bam + // statistics. + file(process.out.bam[0][1]).name, + bam(process.out.bam[0][1], stringency: "silent").getStatistics(exclude:["sorted"]), process.out.log, process.out.fastq, process.out.findAll { key, val -> key.startsWith('versions') } ).match() } - ) } } - test("sarscov2 - [fastq1, fastq2], index, fasta_fai, true, true - cram") { + test("sarscov2 - [fastq1, fastq2], index, fasta_fai, false, true - cram") { config "./cram_crai.config" setup { @@ -527,7 +457,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map + [ + id:'test', + single_end:false, + fasta:'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/sarscov2/genome/genome.fasta' ], // meta map + fasta for cram testing [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) @@ -549,7 +482,9 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.cram[0][1]).name, - file(process.out.crai[0][1]).name + file(process.out.crai[0][1]).name, + cram(process.out.cram[0][1], process.out.cram[0][0].fasta ).getStatistics(exclude:["sorted"]), + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) } @@ -638,7 +573,7 @@ nextflow_process { [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[3] = false //save_unaligned + input[3] = true //save_unaligned input[4] = false //sort """ } diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test.snap b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap index 1585bb13..ac9f561d 100644 --- a/modules/nf-core/bowtie2/align/tests/main.nf.test.snap +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap @@ -1,24 +1,37 @@ { - 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>=1.8.13,<2.0a0 +license: MIT +license_family: MIT +size: 394356 +timestamp: 1787103094046 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h9d15635_7.conda +sha256: 427fd14bcb3b8659796fecc682716617409350fb5a98e5b7b47558a10d1a2fc7 +md5: d942e34ac3920ba83f8b2d0169570187 +depends: +- libzlib >=1.3.2,<2.0a0 +license: BSD-3-Clause +license_family: BSD +size: 615477 +timestamp: 1786599613561 diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/fgumi/filter/environment.yml similarity index 68% rename from modules/nf-core/picard/collectmultiplemetrics/environment.yml rename to modules/nf-core/fgumi/filter/environment.yml index b4ac4fe0..c417e292 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/fgumi/filter/environment.yml @@ -4,5 +4,4 @@ channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/picard - - bioconda::picard=3.4.0 + - "bioconda::fgumi=0.7.0" diff --git a/modules/nf-core/fgumi/filter/fgumi-filter.diff b/modules/nf-core/fgumi/filter/fgumi-filter.diff new file mode 100644 index 00000000..b567503a --- /dev/null +++ b/modules/nf-core/fgumi/filter/fgumi-filter.diff @@ -0,0 +1,23 @@ +Changes in component 'nf-core/fgumi/filter' +'modules/nf-core/fgumi/filter/environment.yml' is unchanged +'modules/nf-core/fgumi/filter/meta.yml' is unchanged +Changes in 'fgumi/filter/main.nf': +--- modules/nf-core/fgumi/filter/main.nf ++++ modules/nf-core/fgumi/filter/main.nf +@@ -8,8 +8,7 @@ + : 'community.wave.seqera.io/library/fgumi:0.6.0--c97194d17da0d1cd'}" + + input: +- tuple val(meta), path(bam) +- tuple val(meta2), path(fasta) ++ tuple val(meta), path(bam), path(fasta) + val min_reads + val keep_rejected + + +'modules/nf-core/fgumi/filter/tests/main.nf.test.snap' is unchanged +'modules/nf-core/fgumi/filter/tests/nextflow.config' is unchanged +'modules/nf-core/fgumi/filter/tests/main.nf.test' is unchanged +'modules/nf-core/fgumi/filter/.conda-lock/linux_amd64-bd-c97194d17da0d1cd_1.txt' is unchanged +'modules/nf-core/fgumi/filter/.conda-lock/linux_arm64-bd-c2c03620f6999cbb_1.txt' is unchanged +************************************************************ diff --git a/modules/nf-core/fgumi/filter/main.nf b/modules/nf-core/fgumi/filter/main.nf new file mode 100644 index 00000000..5c1ca1bf --- /dev/null +++ b/modules/nf-core/fgumi/filter/main.nf @@ -0,0 +1,55 @@ +process FGUMI_FILTER { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' + : 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a'}" + + input: + tuple val(meta), path(bam), path(fasta) + val min_reads + val keep_rejected + + output: + tuple val(meta), path("${prefix}.bam"), emit: bam + tuple val(meta), path("${prefix}.rejects.bam"), emit: rejects, optional: true + tuple val(meta), path("${prefix}.stats.txt"), emit: stats + tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | sed "s/^fgumi //"'), topic: versions, emit: versions_fgumi + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}_consensus_filtered" + def rejects_command = keep_rejected ? "--rejects ${prefix}.rejects.bam" : '' + if ("${bam}" == "${prefix}.bam") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } + + """ + fgumi filter \\ + --input ${bam} \\ + --output ${prefix}.bam \\ + --ref ${fasta} \\ + --min-reads ${min_reads} \\ + --threads ${task.cpus} \\ + --stats ${prefix}.stats.txt \\ + ${rejects_command} \\ + ${args} + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}_consensus_filtered" + def rejects_command = keep_rejected ? "touch ${prefix}.rejects.bam" : '' + if ("${bam}" == "${prefix}.bam") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } + """ + touch ${prefix}.bam + ${rejects_command} + touch ${prefix}.stats.txt + """ +} diff --git a/modules/nf-core/fgumi/filter/meta.yml b/modules/nf-core/fgumi/filter/meta.yml new file mode 100644 index 00000000..a265a477 --- /dev/null +++ b/modules/nf-core/fgumi/filter/meta.yml @@ -0,0 +1,132 @@ +name: "fgumi_filter" +description: | + Filters consensus reads generated by simplex or duplex consensus calling. + This is a high-performance replacement for fgbio FilterConsensusReads. +keywords: + - umi + - filter + - consensus + - bam +tools: + - "fgumi": + description: "High-performance tools for working with UMI-tagged sequencing data." + homepage: "https://github.com/fulcrumgenomics/fgumi" + documentation: "https://docs.rs/fgumi" + tool_dev_url: "https://github.com/fulcrumgenomics/fgumi" + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Consensus BAM file to be filtered + pattern: "*.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + ontologies: + - edam: "http://edamontology.org/format_1929" + - min_reads: + type: integer + description: Minimum number of reads required to keep a consensus read + - keep_rejected: + type: boolean + description: Whether to keep rejected reads in a separate BAM file +output: + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.bam": + type: file + description: Filtered consensus BAM file + pattern: "*.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" + rejects: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.rejects.bam": + type: file + description: Optional BAM file containing reads that were filtered out + pattern: "*.rejects.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" + stats: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.stats.txt": + type: file + description: Optional text file containing filtering statistics + pattern: "*.stats.txt" + ontologies: [] + versions_fgumi: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - 'fgumi --version | sed "s/^fgumi //"': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - 'fgumi --version | sed "s/^fgumi //"': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@sppearce" +maintainers: + - "@sppearce" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb + build_id: bd-595c95b71b3df5bb_1 + scan_id: sc-61ac7030bb5e32a9_1 + linux/amd64: + name: community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a + build_id: bd-d91f99b4cd4aae5a_1 + scan_id: sc-760abd46b15b110e_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55 + build_id: bd-e2a3aedc6034aa55_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data + linux/arm64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b + build_id: bd-72ed3ddc0a890f6b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data + conda: + linux/amd64: + lock_file: modules/nf-core/fgumi/filter/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt + linux/arm64: + lock_file: modules/nf-core/fgumi/filter/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt diff --git a/modules/nf-core/fgumi/filter/tests/main.nf.test b/modules/nf-core/fgumi/filter/tests/main.nf.test new file mode 100644 index 00000000..3c6e646d --- /dev/null +++ b/modules/nf-core/fgumi/filter/tests/main.nf.test @@ -0,0 +1,103 @@ +nextflow_process { + + name "Test Process FGUMI_FILTER" + script "../main.nf" + process "FGUMI_FILTER" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "fgumi" + tag "fgumi/filter" + tag "fgumi/sort" + tag "fgumi/group" + tag "fgumi/simplex" + + setup { + run("FGUMI_SORT") { + script "../../sort/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam', checkIfExists: true) + ] + """ + } + + } + run("FGUMI_GROUP") { + script "../../group/main.nf" + process { + """ + input[0] = FGUMI_SORT.out.bam + input[1] = 'adjacency' + """ + } + } + run("FGUMI_SIMPLEX") { + script "../../simplex/main.nf" + process { + """ + input[0] = FGUMI_GROUP.out.bam + input[1] = 1 + input[2] = false + """ + } + } + } + + test("homo_sapiens - bam") { + + when { + process { + """ + input[0] = FGUMI_SIMPLEX.out.bam + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = 1 + input[3] = false + """ + } + } + + then { + assert process.success + assertAll( + // bam file is non deterministic in its output order + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match() } + ) + } + + } + + test("homo_sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = FGUMI_SIMPLEX.out.bam + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = 1 + input[3] = false + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + + } + +} diff --git a/modules/nf-core/fgumi/filter/tests/main.nf.test.snap b/modules/nf-core/fgumi/filter/tests/main.nf.test.snap new file mode 100644 index 00000000..fd5aa53d --- /dev/null +++ b/modules/nf-core/fgumi/filter/tests/main.nf.test.snap @@ -0,0 +1,76 @@ +{ + "homo_sapiens - bam": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test_consensus_filtered.bam" + ] + ], + "rejects": [ + + ], + "stats": [ + [ + { + "id": "test" + }, + "test_consensus_filtered.stats.txt:md5,4125dfd4096881fdae1b5c927ee5e4a1" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_FILTER", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T15:11:56.996849", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - bam - stub": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test_consensus_filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "rejects": [ + + ], + "stats": [ + [ + { + "id": "test" + }, + "test_consensus_filtered.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_FILTER", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:35:15.853744", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/fgumi/filter/tests/nextflow.config b/modules/nf-core/fgumi/filter/tests/nextflow.config new file mode 100644 index 00000000..2797dd5a --- /dev/null +++ b/modules/nf-core/fgumi/filter/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: FGUMI_SORT { + ext.args = '--order template-coordinate' + } +} diff --git a/modules/nf-core/fgumi/group/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt b/modules/nf-core/fgumi/group/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt new file mode 100644 index 00000000..7e7df88e --- /dev/null +++ b/modules/nf-core/fgumi/group/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt @@ -0,0 +1,1439 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2 +- conda: 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+license_family: BSD +size: 615477 +timestamp: 1786599613561 diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/fgumi/group/environment.yml similarity index 61% rename from modules/nf-core/picard/collectwgsmetrics/environment.yml rename to modules/nf-core/fgumi/group/environment.yml index 186d4a4b..c417e292 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/fgumi/group/environment.yml @@ -4,6 +4,4 @@ channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/picard - - bioconda::picard=3.4.0 - - conda-forge::r-base=4.4.1 + - "bioconda::fgumi=0.7.0" diff --git a/modules/nf-core/fgumi/group/main.nf b/modules/nf-core/fgumi/group/main.nf new file mode 100644 index 00000000..c1fe0c94 --- /dev/null +++ b/modules/nf-core/fgumi/group/main.nf @@ -0,0 +1,52 @@ +process FGUMI_GROUP { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' + : 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a'}" + + input: + tuple val(meta), path(bam) + val strategy + + output: + tuple val(meta), path("*.bam"), emit: bam + tuple val(meta), path("*.family_size_histogram.txt"), emit: histogram + tuple val(meta), path("*.grouping_metrics.txt"), emit: metrics + tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | sed "s/^fgumi //"'), topic: versions, emit: versions_fgumi + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}_umi-grouped" + + if ("${bam}" == "${prefix}.bam") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } + + """ + fgumi group \\ + --input ${bam} \\ + --output ${prefix}.bam \\ + --strategy ${strategy} \\ + --family-size-histogram ${prefix}.family_size_histogram.txt \\ + --grouping-metrics ${prefix}.grouping_metrics.txt \\ + --threads ${task.cpus} \\ + ${args} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}_umi-grouped" + if ("${bam}" == "${prefix}.bam") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } + """ + touch ${prefix}.bam + touch ${prefix}.family_size_histogram.txt + touch ${prefix}.grouping_metrics.txt + """ +} diff --git a/modules/nf-core/fgumi/group/meta.yml b/modules/nf-core/fgumi/group/meta.yml new file mode 100644 index 00000000..79ecdf9a --- /dev/null +++ b/modules/nf-core/fgumi/group/meta.yml @@ -0,0 +1,124 @@ +name: "fgumi_group" +description: | + Groups reads together that appear to have come from the same original molecule. + Reads are grouped by template, and then templates are sorted by the 5' mapping positions + of the reads from the template. Reads that have the same end positions are then sub-grouped + by UMI sequence. This is a high-performance replacement for fgbio GroupReadsByUmi. +keywords: + - umi + - groupreads + - bam +tools: + - "fgumi": + description: "High-performance tools for working with UMI-tagged sequencing data." + homepage: "https://github.com/fulcrumgenomics/fgumi" + documentation: "https://docs.rs/fgumi" + tool_dev_url: "https://github.com/fulcrumgenomics/fgumi" + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads with UMI tags. The file must be coordinate sorted. + pattern: "*.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" + - strategy: + type: string + enum: + - "Identity" + - "Edit" + - "Adjacency" + - "Paired" + description: | + Required argument: defines the UMI assignment strategy. + Must be chosen among: Identity, Edit, Adjacency, Paired. +output: + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: UMI-grouped BAM file + pattern: "*.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" + histogram: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.family_size_histogram.txt": + type: file + description: Optional output of tag family size counts + pattern: "*.family_size_histogram.txt" + metrics: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.grouping_metrics.txt": + type: file + description: Optional output of UMI grouping metrics + pattern: "*.grouping_metrics.txt" + versions_fgumi: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - fgumi --version | sed "s/^fgumi //": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - fgumi --version | sed "s/^fgumi //": + type: eval + description: The expression to obtain the version of the tool +authors: + - "@sppearce" +maintainers: + - "@sppearce" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb + build_id: bd-595c95b71b3df5bb_1 + scan_id: sc-61ac7030bb5e32a9_1 + linux/amd64: + name: community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a + build_id: bd-d91f99b4cd4aae5a_1 + scan_id: sc-760abd46b15b110e_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55 + build_id: bd-e2a3aedc6034aa55_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data + linux/arm64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b + build_id: bd-72ed3ddc0a890f6b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data + conda: + linux/amd64: + lock_file: modules/nf-core/fgumi/group/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt + linux/arm64: + lock_file: modules/nf-core/fgumi/group/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt diff --git a/modules/nf-core/fgumi/group/tests/main.nf.test b/modules/nf-core/fgumi/group/tests/main.nf.test new file mode 100644 index 00000000..54cb685e --- /dev/null +++ b/modules/nf-core/fgumi/group/tests/main.nf.test @@ -0,0 +1,74 @@ +nextflow_process { + + name "Test Process FGUMI_GROUP" + script "../main.nf" + process "FGUMI_GROUP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "fgumi" + tag "fgumi/group" + tag "fgumi/sort" + + test("sarscov2 - bam") { + + setup { + run("FGUMI_SORT") { + script "../../sort/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam', checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = FGUMI_SORT.out.bam + input[1] = 'adjacency' + """ + } + } + + then { + assert process.success + assertAll( + // bam file is non deterministic in its output order + { assert snapshot(sanitizeOutput(process.out, readsMD5Keys: ["bam"])).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam', checkIfExists: true) + ] + input[1] = 'adjacency' + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + + } + +} diff --git a/modules/nf-core/fgumi/group/tests/main.nf.test.snap b/modules/nf-core/fgumi/group/tests/main.nf.test.snap new file mode 100644 index 00000000..ee9f8ec6 --- /dev/null +++ b/modules/nf-core/fgumi/group/tests/main.nf.test.snap @@ -0,0 +1,86 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test_umi-grouped.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "histogram": [ + [ + { + "id": "test" + }, + "test_umi-grouped.family_size_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "id": "test" + }, + "test_umi-grouped.grouping_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_GROUP", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:35:28.978907", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "sarscov2 - bam": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test_umi-grouped.bam:md5Reads,8ac937a6e6583e8e97f3a5f5149817a5" + ] + ], + "histogram": [ + [ + { + "id": "test" + }, + "test_umi-grouped.family_size_histogram.txt:md5,f6fcd67cb38e4976a9c458c27a30a798" + ] + ], + "metrics": [ + [ + { + "id": "test" + }, + "test_umi-grouped.grouping_metrics.txt:md5,a5f75e3e390e30791a636fed355e0afd" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_GROUP", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T13:36:18.378156", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/fgumi/group/tests/nextflow.config b/modules/nf-core/fgumi/group/tests/nextflow.config new file mode 100644 index 00000000..2797dd5a --- /dev/null +++ b/modules/nf-core/fgumi/group/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: FGUMI_SORT { + ext.args = '--order template-coordinate' + } +} diff --git a/modules/nf-core/fgumi/merge/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt b/modules/nf-core/fgumi/merge/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt new file mode 100644 index 00000000..7e7df88e --- /dev/null +++ b/modules/nf-core/fgumi/merge/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt @@ -0,0 +1,1439 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: 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+license_family: BSD +size: 615477 +timestamp: 1786599613561 diff --git a/modules/nf-core/fgumi/merge/environment.yml b/modules/nf-core/fgumi/merge/environment.yml new file mode 100644 index 00000000..c417e292 --- /dev/null +++ b/modules/nf-core/fgumi/merge/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::fgumi=0.7.0" diff --git a/modules/nf-core/fgumi/merge/main.nf b/modules/nf-core/fgumi/merge/main.nf new file mode 100644 index 00000000..66dd135a --- /dev/null +++ b/modules/nf-core/fgumi/merge/main.nf @@ -0,0 +1,37 @@ +process FGUMI_MERGE { + tag "${meta.id}" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' + : 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a'}" + + input: + tuple val(meta), path(bams, stageAs: "?/*") + + output: + tuple val(meta), path("*.bam"), emit: bam + tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | sed "s/^fgumi //"'), topic: versions, emit: versions_fgumi + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + fgumi \\ + merge \\ + --output ${prefix}.bam \\ + --threads ${task.cpus} \\ + ${args} \\ + ${bams} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + """ +} diff --git a/modules/nf-core/fgumi/merge/meta.yml b/modules/nf-core/fgumi/merge/meta.yml new file mode 100644 index 00000000..e674c4d9 --- /dev/null +++ b/modules/nf-core/fgumi/merge/meta.yml @@ -0,0 +1,92 @@ +name: "fgumi_merge" +description: Merge pre-sorted BAM files into a single sorted BAM +keywords: + - merge + - bam + - alignment + - sort +tools: + - "fgumi": + description: "High-performance tools for UMI-tagged sequencing data." + homepage: "https://github.com/fulcrumgenomics/fgumi" + documentation: "https://fgumi.readthedocs.io/" + tool_dev_url: "https://github.com/fulcrumgenomics/fgumi" + licence: ["MIT"] + identifier: biotools:fgumi + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - bams: + type: file + description: Multiple sorted BAM files to merge (all must be sorted in the same order) + pattern: "*.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" # BAM + +output: + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.bam": + type: file + description: Merged BAM file + pattern: "*.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" # BAM + versions_fgumi: + - - "${task.process}": + type: string + description: The name of the process + - "fgumi": + type: string + description: The name of the tool + - 'fgumi --version | sed "s/^fgumi //"': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - fgumi: + type: string + description: The name of the tool + - fgumi --version | sed "s/^fgumi //": + type: eval + description: The expression to obtain the version of the tool +authors: + - "@sppearce" +maintainers: + - "@sppearce" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb + build_id: bd-595c95b71b3df5bb_1 + scan_id: sc-61ac7030bb5e32a9_1 + linux/amd64: + name: community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a + build_id: bd-d91f99b4cd4aae5a_1 + scan_id: sc-760abd46b15b110e_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55 + build_id: bd-e2a3aedc6034aa55_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data + linux/arm64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b + build_id: bd-72ed3ddc0a890f6b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data + conda: + linux/amd64: + lock_file: modules/nf-core/fgumi/merge/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt + linux/arm64: + lock_file: modules/nf-core/fgumi/merge/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt diff --git a/modules/nf-core/fgumi/merge/tests/main.nf.test b/modules/nf-core/fgumi/merge/tests/main.nf.test new file mode 100644 index 00000000..869c5b8e --- /dev/null +++ b/modules/nf-core/fgumi/merge/tests/main.nf.test @@ -0,0 +1,134 @@ +nextflow_process { + + name "Test Process FGUMI_MERGE" + script "../main.nf" + process "FGUMI_MERGE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "fgumi" + tag "fgumi/merge" + + test("homo_sapiens - one bam") { + + when { + params { + module_args = "--order coordinate" + } + process { + """ + input[0] = [ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("homo_sapiens - multiple bams - template coordinate") { + + when { + params { + module_args = "--order coordinate" + } + process { + """ + input[0] = [ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("homo_sapiens - multiple bams - coordinate sorted") { + + when { + params { + module_args = "--order coordinate" + } + process { + """ + input[0] = [ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("homo_sapiens - multiple bams - stub") { + + options "-stub" + + when { + params { + module_args = "" + } + process { + """ + input[0] = [ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + + } + +} diff --git a/modules/nf-core/fgumi/merge/tests/main.nf.test.snap b/modules/nf-core/fgumi/merge/tests/main.nf.test.snap new file mode 100644 index 00000000..4b1a5bb2 --- /dev/null +++ b/modules/nf-core/fgumi/merge/tests/main.nf.test.snap @@ -0,0 +1,85 @@ +{ + "homo_sapiens - multiple bams - coordinate sorted": { + "content": [ + "c4525b95f05075208347295e6a1fb232", + { + "versions_fgumi": [ + [ + "FGUMI_MERGE", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:35:46.660043", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - multiple bams - stub": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_MERGE", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:35:51.370051", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - one bam": { + "content": [ + "2f11e4fe3390b8ad0a1852616fd1da04", + { + "versions_fgumi": [ + [ + "FGUMI_MERGE", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:35:36.483872", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - multiple bams - template coordinate": { + "content": [ + "c4525b95f05075208347295e6a1fb232", + { + "versions_fgumi": [ + [ + "FGUMI_MERGE", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:35:41.630868", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/fgumi/merge/tests/nextflow.config b/modules/nf-core/fgumi/merge/tests/nextflow.config new file mode 100644 index 00000000..e79a9602 --- /dev/null +++ b/modules/nf-core/fgumi/merge/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: FGUMI_MERGE { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/fgumi/simplex/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt b/modules/nf-core/fgumi/simplex/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt new file mode 100644 index 00000000..7e7df88e --- /dev/null +++ b/modules/nf-core/fgumi/simplex/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt @@ -0,0 +1,1439 @@ + +version: 6 +environments: +default: +channels: +- url: 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+license_family: BSD +size: 615477 +timestamp: 1786599613561 diff --git a/modules/nf-core/fgumi/simplex/environment.yml b/modules/nf-core/fgumi/simplex/environment.yml new file mode 100644 index 00000000..c417e292 --- /dev/null +++ b/modules/nf-core/fgumi/simplex/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::fgumi=0.7.0" diff --git a/modules/nf-core/fgumi/simplex/fgumi-simplex.diff b/modules/nf-core/fgumi/simplex/fgumi-simplex.diff new file mode 100644 index 00000000..779c9feb --- /dev/null +++ b/modules/nf-core/fgumi/simplex/fgumi-simplex.diff @@ -0,0 +1,24 @@ +Changes in component 'nf-core/fgumi/simplex' +'modules/nf-core/fgumi/simplex/environment.yml' is unchanged +'modules/nf-core/fgumi/simplex/meta.yml' is unchanged +Changes in 'fgumi/simplex/main.nf': +--- modules/nf-core/fgumi/simplex/main.nf ++++ modules/nf-core/fgumi/simplex/main.nf +@@ -8,9 +8,7 @@ + : 'community.wave.seqera.io/library/fgumi:0.6.0--c97194d17da0d1cd'}" + + input: +- tuple val(meta), path(grouped_bam) +- val min_reads +- val keep_rejected ++ tuple val(meta), path(grouped_bam), val(min_reads), val(keep_rejected) + + output: + tuple val(meta), path("${prefix}.bam"), emit: bam + +'modules/nf-core/fgumi/simplex/tests/main.nf.test.snap' is unchanged +'modules/nf-core/fgumi/simplex/tests/nextflow.config' is unchanged +'modules/nf-core/fgumi/simplex/tests/main.nf.test' is unchanged +'modules/nf-core/fgumi/simplex/.conda-lock/linux_amd64-bd-c97194d17da0d1cd_1.txt' is unchanged +'modules/nf-core/fgumi/simplex/.conda-lock/linux_arm64-bd-c2c03620f6999cbb_1.txt' is unchanged +************************************************************ diff --git a/modules/nf-core/fgumi/simplex/main.nf b/modules/nf-core/fgumi/simplex/main.nf new file mode 100644 index 00000000..23824bb7 --- /dev/null +++ b/modules/nf-core/fgumi/simplex/main.nf @@ -0,0 +1,52 @@ +process FGUMI_SIMPLEX { + tag "${meta.id}" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data' + : 'community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a'}" + + input: + tuple val(meta), path(grouped_bam), val(min_reads), val(keep_rejected) + + output: + tuple val(meta), path("${prefix}.bam"), emit: bam + tuple val(meta), path("${prefix}.rejects.bam"), emit: rejects, optional: true + tuple val(meta), path("${prefix}.stats.txt"), emit: stats + tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | sed "s/^fgumi //"'), topic: versions, emit: versions_fgumi + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}_simplex_unmapped" + def rejects_command = keep_rejected ? "--rejects ${prefix}.rejects.bam" : '' + + if ("${grouped_bam}" == "${prefix}.bam") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } + + """ + fgumi simplex \\ + --input ${grouped_bam} \\ + --output ${prefix}.bam \\ + --min-reads ${min_reads} \\ + --threads ${task.cpus} \\ + --stats ${prefix}.stats.txt \\ + ${rejects_command} \\ + ${args} + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}_simplex_unmapped" + if ("${grouped_bam}" == "${prefix}.bam") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } + """ + touch ${prefix}.bam + touch ${prefix}.rejects.bam + touch ${prefix}.stats.txt + """ +} diff --git a/modules/nf-core/fgumi/simplex/meta.yml b/modules/nf-core/fgumi/simplex/meta.yml new file mode 100644 index 00000000..1404c28c --- /dev/null +++ b/modules/nf-core/fgumi/simplex/meta.yml @@ -0,0 +1,122 @@ +name: "fgumi_simplex" +description: | + Calls simplex consensus sequences from reads with the same unique molecular tag. + This is a high-performance replacement for fgbio CallMolecularConsensusReads. +keywords: + - umi + - consensus + - simplex + - bam +tools: + - "fgumi": + description: "High-performance tools for working with UMI-tagged sequencing data." + homepage: "https://github.com/fulcrumgenomics/fgumi" + documentation: "https://docs.rs/fgumi" + tool_dev_url: "https://github.com/fulcrumgenomics/fgumi" + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - grouped_bam: + type: file + description: | + The input SAM or BAM file, grouped by UMIs + pattern: "*.{bam,sam}" + ontologies: + - edam: "http://edamontology.org/format_2572" + - min_reads: + type: integer + description: Minimum number of original reads to build each consensus read. + - keep_rejected: + type: boolean + description: If true, output rejected reads to a separate BAM file +output: + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.bam": + type: file + description: | + Output SAM or BAM file with simplex consensus reads. + pattern: "*.{bam,sam}" + ontologies: + - edam: "http://edamontology.org/format_2572" + rejects: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.rejects.bam": + type: file + description: Optional BAM file containing reads that were rejected + pattern: "*.rejects.bam" + ontologies: + - edam: "http://edamontology.org/format_2572" # BAM + stats: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.stats.txt": + type: file + description: Optional text file containing consensus statistics + pattern: "*.stats.txt" + versions_fgumi: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - fgumi --version | sed "s/^fgumi //": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fgumi: + type: string + description: The tool name + - fgumi --version | sed "s/^fgumi //": + type: eval + description: The expression to obtain the version of the tool +authors: + - "@sppearce" +maintainers: + - "@sppearce" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/fgumi:0.7.0--d91f99b4cd4aae5a + build_id: bd-d91f99b4cd4aae5a_1 + scan_id: sc-760abd46b15b110e_1 + linux/arm64: + name: community.wave.seqera.io/library/fgumi:0.7.0--595c95b71b3df5bb + build_id: bd-595c95b71b3df5bb_1 + scan_id: sc-61ac7030bb5e32a9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--e2a3aedc6034aa55 + build_id: bd-e2a3aedc6034aa55_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/99/99c92db2efcbcc4d20f2541060e09ed0f5a4338927f4a2ae3ab683de585efeb6/data + linux/arm64: + name: oras://community.wave.seqera.io/library/fgumi:0.7.0--72ed3ddc0a890f6b + build_id: bd-72ed3ddc0a890f6b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a8a09ab5b500dc5a4ff93fe835b6e8afa4e3636b8075771b1e011bc2dad16aa0/data + conda: + linux/amd64: + lock_file: modules/nf-core/fgumi/simplex/.conda-lock/linux_amd64-bd-d91f99b4cd4aae5a_1.txt + linux/arm64: + lock_file: modules/nf-core/fgumi/simplex/.conda-lock/linux_arm64-bd-595c95b71b3df5bb_1.txt diff --git a/modules/nf-core/fgumi/simplex/tests/main.nf.test b/modules/nf-core/fgumi/simplex/tests/main.nf.test new file mode 100644 index 00000000..a0d567d1 --- /dev/null +++ b/modules/nf-core/fgumi/simplex/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_process { + + name "Test Process FGUMI_SIMPLEX" + script "../main.nf" + process "FGUMI_SIMPLEX" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "fgumi" + tag "fgumi/simplex" + tag "fgumi/sort" + tag "fgumi/group" + + setup { + run("FGUMI_SORT") { + script "../../sort/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam', checkIfExists: true) + ] + """ + } + } + run("FGUMI_GROUP") { + script "../../group/main.nf" + process { + """ + input[0] = FGUMI_SORT.out.bam + input[1] = 'adjacency' + """ + } + } + } + + test("homo_sapiens - bam") { + + when { + process { + """ + input[0] = FGUMI_GROUP.out.bam + input[1] = 1 + input[2] = false + """ + } + } + + then { + assert process.success + assertAll( + // bam file is non deterministic in its output order + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match() } + ) + } + + } + + test("homo_sapiens - bam - with rejects") { + + when { + process { + """ + input[0] = FGUMI_GROUP.out.bam + input[1] = 1 + input[2] = true + """ + } + } + + then { + assert process.success + assertAll( + // bam file is non deterministic in its output order + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ['bam', 'rejects'])).match() } + ) + } + + } + + test("homo_sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam', checkIfExists: true) + ] + input[1] = 1 + input[2] = false + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/fgumi/simplex/tests/main.nf.test.snap b/modules/nf-core/fgumi/simplex/tests/main.nf.test.snap new file mode 100644 index 00000000..a71ae515 --- /dev/null +++ b/modules/nf-core/fgumi/simplex/tests/main.nf.test.snap @@ -0,0 +1,154 @@ +{ + "homo_sapiens - bam - with rejects": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.bam" + ] + ], + "rejects": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.rejects.bam" + ] + ], + "stats": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.stats.txt:md5,76e4e3c4f1d83724432642063472daf1" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_SIMPLEX", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:36:12.185776", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - bam": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.bam" + ] + ], + "rejects": [ + + ], + "stats": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.stats.txt:md5,76e4e3c4f1d83724432642063472daf1" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_SIMPLEX", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T15:18:53.642256", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.rejects.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + "FGUMI_SIMPLEX", + "fgumi", + "0.7.0" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "rejects": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.rejects.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test" + }, + "test_simplex_unmapped.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_fgumi": [ + [ + "FGUMI_SIMPLEX", + "fgumi", + "0.7.0" + ] + ] + } + ], + "timestamp": "2026-08-25T12:36:25.931142", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/fgumi/simplex/tests/nextflow.config b/modules/nf-core/fgumi/simplex/tests/nextflow.config new file mode 100644 index 00000000..2797dd5a --- /dev/null +++ b/modules/nf-core/fgumi/simplex/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: FGUMI_SORT { + ext.args = '--order template-coordinate' + } +} diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt new file mode 100644 index 00000000..2a91c22d --- /dev/null +++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt @@ -0,0 +1,1526 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: 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f787dbe1..00000000 --- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt +++ /dev/null @@ -1,125 +0,0 @@ - -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-aarch64 -@EXPLICIT -https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958 -https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d -https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6 -https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d -https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1 -https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc -https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda#a21644fc4a83da26452a718dc9468d5f -https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.5-hfae3067_0.conda#05d1e0b30acd816a192c03dc6e164f4d -https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda#2f364feefb6a7c00423e80dcb12db62a -https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda#76298a9e6d71ee6e832a8d0d7373b261 -https://conda.anaconda.org/conda-forge/linux-aarch64/libmpdec-4.0.0-he30d5cf_1.conda#7b9813e885482e3ccb1fa212b86d7fd0 -https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.53.0-h022381a_0.conda#86db4036fd08bf34e991bf48a8af405d -https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.42-h1022ec0_0.conda#a0b5de740d01c390bdbb46d7503c9fab -https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.5-ha32ae93_3.conda#182afabe009dc78d8b73100255ee6868 -https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73 -https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.2-h546c87b_0.conda#3b129669089e4d6a5c6871dbb4669b99 -https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4 -https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-hb682ff5_0.conda#3d49cad61f829f4f0e0611547a9cda12 -https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda#7fc6affb9b01e567d2ef1d05b84aa6ed -https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610 -https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.4-hfd9ac0a_100_cp314.conda#3cfbe780f0f51cc8cba41db9f8a28bfe -https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda#f111d4cfaf1fe9496f386bc98ae94452 -https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda#e4e60721757979d01d3964122f674959 -https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda#aaa2a381ccc56eac91d63b6c1240312f -https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda#0caa1af407ecff61170c9437a808404d -https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda#edd329d7d3a4ab45dcf905899a7a6115 -https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda#2934f256a8acfe48f6ebb4fce6cde29c -https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda#c6b0543676ecb1fb2d7643941fe375f2 -https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda#a2ac7763a9ac75055b68f325d3255265 -https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_18.conda#f56573d05e3b735cb03efeb64a15f388 -https://conda.anaconda.org/conda-forge/linux-aarch64/brotli-python-1.2.0-py314h352cb57_1.conda#a1b5c571a0923a205d663d8678df4792 -https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5 -https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda#a9167b9571f3baa9d448faa2139d1089 -https://conda.anaconda.org/conda-forge/noarch/click-8.3.2-pyhc90fa1f_0.conda#4d18bc3af7cfcea97bd817164672a08c -https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda#7fe569c10905402ed47024fc481bb371 -https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda#b866ff7007b934d564961066c8195983 -https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda#a2c1eeadae7a309daed9d62c96012a2b -https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran5-15.2.0-h1b7bec0_18.conda#574d88ce3348331e962cfa5ed451b247 -https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran-15.2.0-he9431aa_18.conda#41f261f5e4e2e8cbd236c2f1f15dae1b -https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.32-pthreads_h9d3fd7e_0.conda#5d2ce5cf40443d055ec6d33840192265 -https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-6_haddc8a3_openblas.conda#652bb20bb4618cacd11e17ae070f47ce -https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-6_hd72aa62_openblas.conda#939e300b110db241a96a1bed438c315b -https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-6_h88aeb00_openblas.conda#e23a27b52fb320687239e2c5ae4d7540 -https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.3-py314haac167e_0.conda#25d896c331481145720a21e5145fad65 -https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda#071cf7b0ce333c81718b054066c15102 -https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.7.5-hfae3067_0.conda#d2bb0c889d94f2fdc5856392c3002976 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 -https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.58-h1abf092_0.conda#f51503ac45a4888bce71af9027a2ecc9 -https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype6-2.14.3-hdae7a39_0.conda#b99ed99e42dafb27889483b3098cace7 -https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype-2.14.3-h8af1aa0_0.conda#a229e22d4d8814a07702b0919d8e6701 -https://conda.anaconda.org/conda-forge/linux-aarch64/fontconfig-2.17.1-hba86a56_0.conda#0fed1ff55f4938a65907f3ecf62609db -https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681 -https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda#0a802cb9888dd14eeefc611f05c40b6e -https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda#8e6923fc12f1fe8f8c4e5c9f343256ac -https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda#164fc43f0b53b6e3a7bc7dce5e4f1dc9 -https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda#daddf757c3ecd6067b9af1df1f25d89e -https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda#fb7130c190f9b4ec91219840a05ba3ac -https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda#e1c36c6121a7c9c76f2f148f1e83b983 -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda#080594bf4493e6bae2607e65390c520a -https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda#e5de3c36dd548b35ff2a8aa49208dcb3 -https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda#04558c96691bed63104678757beb4f8d -https://conda.anaconda.org/conda-forge/linux-aarch64/rpds-py-0.30.0-py314h02b7a91_0.conda#e7f6ed9e60043bb5cbcc527764897f0d -https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda#870293df500ca7e18bedefa5838a22ab -https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda#439cd0f567d697b20a8f45cb70a1005a -https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda#ada41c863af263cc4c5fcbaff7c3e4dc -https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda#4feebd0fbf61075a1a9c2e9b3936c257 -https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2#7b08314a6867a9d5648a1c3265e9eb8e -https://conda.anaconda.org/conda-forge/linux-aarch64/nspr-4.38-h3ad9384_0.conda#6dd4f07147774bf720075a210f8026b9 -https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda#4540f9570d12db2150f42ba036154552 -https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.0-he8854b5_0.conda#ad8164bdeece883b825c50639c0c4725 -https://conda.anaconda.org/conda-forge/linux-aarch64/kaleido-core-0.2.1-he5a581e_0.tar.bz2#4f0d284f5d11e04277b552eb1c172c7f -https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda#a85ba48648f6868016f2741fd9170250 -https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda#d13423b06447113a90b5b1366d4da171 -https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda#a9138815598fe6b91a1d6782ca657b0c -https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda#24e92d0942c799db387f5c9d7b81f1af -https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda#8c6fd84f9c87ac00636007c6131e457d -https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda#bb960f01525b5e001608afef9d47b79c -https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda#bb5a90c93e3bac3d5690acf76b4a6386 -https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda#1c246e1105000c3660558459e2fd6d43 -https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda#bff06dcde4a707339d66d45d96ceb2e2 -https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda#cd14ee5cca2464a425b1dbfc24d90db2 -https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda#ba0a9221ce1063f31692c07370d062f3 -https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda#592132998493b3ff25fd7479396e8351 -https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964 -https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2 -https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8 -https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c -https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b -https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684 -https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98 -https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a -https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910 -https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34 -https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372 -https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7 -https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88 -https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58 -https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc -https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240 -https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6 -https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98 -https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c -https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2 -https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac -https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130 -https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59 -https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0 -https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66 -https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9 -https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a -https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864 -https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6 -https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206 -https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b -https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873 -https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f -https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 37e7612d..7a970e2b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.34 + - bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index e80e8cd8..711983ed 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,9 +3,7 @@ process MULTIQC { label 'process_single' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' - : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" + container "quay.io/cmgg/multiqc_cmgg:0.0.6-multiqc-v1.35" input: tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 2facc627..27ce18d8 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt linux/arm64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 - build_id: bd-db7c73dae76bc9e6_1 - scan_id: sc-66fc7138dbf1cf48_1 + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 - build_id: bd-d167b8012595a136_1 - scan_id: sc-ac701dfa631a2af9_1 + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 - build_id: bd-4fc8657c816047c0_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 - build_id: bd-7fbd82d945c06726_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff new file mode 100644 index 00000000..d20f7de4 --- /dev/null +++ b/modules/nf-core/multiqc/multiqc.diff @@ -0,0 +1,25 @@ +Changes in component 'nf-core/multiqc' +'modules/nf-core/multiqc/environment.yml' is unchanged +'modules/nf-core/multiqc/meta.yml' is unchanged +Changes in 'multiqc/main.nf': +--- modules/nf-core/multiqc/main.nf ++++ modules/nf-core/multiqc/main.nf +@@ -3,9 +3,7 @@ + label 'process_single' + + conda "${moduleDir}/environment.yml" +- container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container +- ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' +- : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" ++ container "quay.io/cmgg/multiqc_cmgg:0.0.6-multiqc-v1.35" + + input: + tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) + +'modules/nf-core/multiqc/tests/main.nf.test.snap' is unchanged +'modules/nf-core/multiqc/tests/nextflow.config' is unchanged +'modules/nf-core/multiqc/tests/main.nf.test' is unchanged +'modules/nf-core/multiqc/tests/custom_prefix.config' is unchanged +'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' is unchanged +'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' is unchanged +************************************************************ diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7c2f370f..44899216 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -81,7 +81,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -175,7 +175,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -221,7 +221,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -314,7 +314,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -408,7 +408,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } diff --git a/modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt b/modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt deleted file mode 100644 index e2883507..00000000 --- a/modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt +++ /dev/null @@ -1,131 +0,0 @@ - -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-64 -@EXPLICIT -https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882 -https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de -https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885 -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec -https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6 -https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda#49f570f3bc4c874a06ea69b7225753af -https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a360c33a5abe61c07959e449fa1453eb -https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb -https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda#2c21e66f50753a083cbe6b80f38268fa -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda#1b08cd684f34175e4514474793d44bcb -https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda#c80d8a3b84358cb967fa81e7075fbc8a -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.0-hf4e2dac_0.conda#810d83373448da85c3f673fbcb7ad3a3 -https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda#38ffe67b78c9d4de527be8315e5ada2c -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 -https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0 -https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4 -https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec -https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab -https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610 -https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-habeac84_100_cp314.conda#a443f87920815d41bfe611296e507995 -https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda#f111d4cfaf1fe9496f386bc98ae94452 -https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda#e4e60721757979d01d3964122f674959 -https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda#aaa2a381ccc56eac91d63b6c1240312f -https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda#0caa1af407ecff61170c9437a808404d -https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda#edd329d7d3a4ab45dcf905899a7a6115 -https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda#2934f256a8acfe48f6ebb4fce6cde29c -https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda#c6b0543676ecb1fb2d7643941fe375f2 -https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda#a2ac7763a9ac75055b68f325d3255265 -https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda#8910d2c46f7e7b519129f486e0fe927a -https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5 -https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda#a9167b9571f3baa9d448faa2139d1089 -https://conda.anaconda.org/conda-forge/noarch/click-8.3.2-pyhc90fa1f_0.conda#4d18bc3af7cfcea97bd817164672a08c -https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda#7fe569c10905402ed47024fc481bb371 -https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda#b866ff7007b934d564961066c8195983 -https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda#a2c1eeadae7a309daed9d62c96012a2b -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda#646855f357199a12f02a87382d429b75 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda#9063115da5bc35fdc3e1002e69b9ef6e -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.32-pthreads_h94d23a6_0.conda#89d61bc91d3f39fda0ca10fcd3c68594 -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-6_h4a7cf45_openblas.conda#6d6d225559bfa6e2f3c90ee9c03d4e2e -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-6_h0358290_openblas.conda#36ae340a916635b97ac8a0655ace2a35 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-6_h47877c9_openblas.conda#881d801569b201c2e753f03c84b85e15 -https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda#36f5b7eb328bdc204954a2225cf908e2 -https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda#071cf7b0ce333c81718b054066c15102 -https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.5-hecca717_0.conda#7de50d165039df32d38be74c1b34a910 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 -https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.58-h421ea60_0.conda#eba48a68a1a2b9d3c0d9511548db85db -https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h73754d4_0.conda#fb16b4b69e3f1dcfe79d80db8fd0c55d -https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.3-ha770c72_0.conda#e289f3d17880e44b633ba911d57a321b -https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.17.1-h27c8c51_0.conda#867127763fbe935bab59815b6e0b7b5c -https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681 -https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda#0a802cb9888dd14eeefc611f05c40b6e -https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda#8e6923fc12f1fe8f8c4e5c9f343256ac -https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda#164fc43f0b53b6e3a7bc7dce5e4f1dc9 -https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda#daddf757c3ecd6067b9af1df1f25d89e -https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda#fb7130c190f9b4ec91219840a05ba3ac -https://conda.anaconda.org/bioconda/linux-64/illumina-interop-1.9.0-h503566f_0.conda#7299cd17a6adac3294ca2d7938377bd4 -https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda#e1c36c6121a7c9c76f2f148f1e83b983 -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda#080594bf4493e6bae2607e65390c520a 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+timestamp: 1764777145593 diff --git a/modules/nf-core/multiqcsav/environment.yml b/modules/nf-core/multiqcsav/environment.yml index b95a2972..b190a347 100644 --- a/modules/nf-core/multiqcsav/environment.yml +++ b/modules/nf-core/multiqcsav/environment.yml @@ -5,9 +5,9 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/multiqc - - bioconda::multiqc=1.34 + - bioconda::multiqc=1.35 # renovate: datasource=conda depName=bioconda/multiqc_sav - bioconda::multiqc_sav=0.2.0 - - pip=25.3 + - pip=26.1.1 - pip: - interop==1.9.0 diff --git a/modules/nf-core/multiqcsav/main.nf b/modules/nf-core/multiqcsav/main.nf index 5d25de8f..09846f59 100644 --- a/modules/nf-core/multiqcsav/main.nf +++ b/modules/nf-core/multiqcsav/main.nf @@ -4,8 +4,8 @@ process MULTIQCSAV { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4590c19f294469392d1bd2689eb9d4a06f18d20f64c5dbc0bbc17473c9941b4e/data' - : 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:644a84cef31cc4aa'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c1311ac2bfb96d77487985fce321b25bbea85f574f9932b827ed6cafe7f75963/data' + : 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9b10d606ce2f36b6'}" input: tuple val(meta), path(xml), path(interop_bin, stageAs: "InterOp/*"), path(extra_multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqcsav/meta.yml b/modules/nf-core/multiqcsav/meta.yml index 1bef87b5..1e94f179 100644 --- a/modules/nf-core/multiqcsav/meta.yml +++ b/modules/nf-core/multiqcsav/meta.yml @@ -112,24 +112,24 @@ output: - multiqc --version | sed "s/.* //g": type: eval description: The expression to obtain the version of the tool - versions_interop: + versions_multiqcsav: - - ${task.process}: type: string description: The process the versions were collected from - - interop: + - multiqcsav: type: string - description: The tool name - - python -c "import interop; print(interop.__version__)": + description: The name of the tool + - python -c "import multiqc_sav; print(multiqc_sav.__version__)": type: eval description: The expression to obtain the version of the tool - versions_multiqcsav: + versions_interop: - - ${task.process}: type: string description: The process the versions were collected from - - multiqcsav: + - interop: type: string - description: The name of the tool - - python -c "import multiqc_sav; print(multiqc_sav.__version__)": + description: The tool name + - python -c "import interop; print(interop.__version__)": type: eval description: The expression to obtain the version of the tool authors: @@ -140,24 +140,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt + lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-9b10d606ce2f36b6_1.txt linux/arm64: - lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-039d1ec6b47ba325_1.txt + lock_file: modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-077315907ed11315_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:644a84cef31cc4aa - build_id: bd-644a84cef31cc4aa_1 - scan_id: sc-253553e37f233660_1 + name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9b10d606ce2f36b6 + build_id: bd-9b10d606ce2f36b6_1 + scan_id: sc-e07d8899984fea53_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:039d1ec6b47ba325 - build_id: bd-039d1ec6b47ba325_1 - scan_id: sc-1c30a1d921d59ec5_1 + name: community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:077315907ed11315 + build_id: bd-077315907ed11315_1 + scan_id: sc-bd28ba4987c53bbe_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9ebe780f2738c655 - build_id: bd-9ebe780f2738c655_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4590c19f294469392d1bd2689eb9d4a06f18d20f64c5dbc0bbc17473c9941b4e/data + name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:a26da1aa4e8d32a6 + build_id: bd-a26da1aa4e8d32a6_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c1311ac2bfb96d77487985fce321b25bbea85f574f9932b827ed6cafe7f75963/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:fc57bb53140baade - build_id: bd-fc57bb53140baade_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b047611068a4009d62d8352e8bb4ab27fa993708a82c029f115e6758b2e44bec/data + name: oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:d1ed21d66511158d + build_id: bd-d1ed21d66511158d_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/05/053f6d8c55b57e04b654070a3bd6eaa90685590158019d35c16092d301b80cb1/data diff --git a/modules/nf-core/multiqcsav/tests/main.nf.test.snap b/modules/nf-core/multiqcsav/tests/main.nf.test.snap index f0a8f3f4..603248d1 100644 --- a/modules/nf-core/multiqcsav/tests/main.nf.test.snap +++ b/modules/nf-core/multiqcsav/tests/main.nf.test.snap @@ -120,7 +120,7 @@ [ "MULTIQCSAV", "multiqc", - "1.34" + "1.35" ] ], "versions_interop": [ @@ -180,7 +180,7 @@ [ "MULTIQCSAV", "multiqc", - "1.34" + "1.35" ] ], "versions_interop": [ diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf deleted file mode 100644 index 17a2736c..00000000 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ /dev/null @@ -1,68 +0,0 @@ -process PICARD_COLLECTHSMETRICS { - tag "${meta.id}" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: - tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "bait/*"), path(target_intervals, stageAs: "target/*") ,path(fasta) ,path(fai) ,path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - - def avail_mem = 3072 - if (!task.memory) { - log.info('[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') - } - else { - avail_mem = (task.memory.mega * 0.8).intValue() - } - - def bait_interval_list = bait_intervals - def bait_intervallist_cmd = "" - if (bait_intervals =~ /.(bed|bed.gz)$/) { - bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") - bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - - def target_interval_list = target_intervals - def target_intervallist_cmd = "" - if (target_intervals =~ /.(bed|bed.gz)$/) { - target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") - target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - """ - export TMP=\$PWD - ${bait_intervallist_cmd} - ${target_intervallist_cmd} - - picard \\ - -Xmx${avail_mem}M \\ - CollectHsMetrics \\ - ${args} \\ - ${reference} \\ - --BAIT_INTERVALS ${bait_interval_list} \\ - --TARGET_INTERVALS ${target_interval_list} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics \\ - --TMP_DIR . - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.CollectHsMetrics.coverage_metrics - """ -} diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml deleted file mode 100644 index 89bc502c..00000000 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ /dev/null @@ -1,129 +0,0 @@ -name: picard_collecthsmetrics -description: Collects hybrid-selection (HS) metrics for a SAM or BAM file. -keywords: - - alignment - - metrics - - statistics - - insert - - hybrid-selection - - quality - - bam -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - tool_dev_url: https://github.com/broadinstitute/picard/ - licence: ["MIT"] - identifier: biotools:picard_tools -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: An aligned BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: [] - - bai: - type: file - description: Optional aligned BAM/CRAM/SAM file index - pattern: "*.{bai,crai,sai}" - ontologies: [] - - bait_intervals: - type: file - description: An interval file that contains the locations of the baits used. - pattern: "*.{interval_list,bed,bed.gz}" - ontologies: [] - - target_intervals: - type: file - description: An interval file that contains the locations of the targets. - pattern: "*.{interval_list,bed,bed.gz}" - ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref: - type: file - description: | - A reference file to calculate dropout metrics measuring reduced representation of reads. - Optional input. - pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" - ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref_fai: - type: file - description: Index of reference file. Only needed when reference is supplied. - pattern: "*.fai" - ontologies: [] - - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref_dict: - type: file - description: Sequence dictionary of FASTA file. Only needed when bed interval - lists are supplied. - pattern: "*.dict" - ontologies: [] - - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - ref_gzi: - type: file - description: Index of reference file. Only needed when gzipped reference is supplied. - pattern: "*.gzi" - ontologies: [] -output: - metrics: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*_metrics": - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - ontologies: [] - versions_picard: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool -authors: - - "@projectoriented" - - "@matthdsm" -maintainers: - - "@projectoriented" - - "@matthdsm" diff --git a/modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff b/modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff deleted file mode 100644 index f9b0281a..00000000 --- a/modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff +++ /dev/null @@ -1,62 +0,0 @@ -Changes in component 'nf-core/picard/collecthsmetrics' -'modules/nf-core/picard/collecthsmetrics/environment.yml' is unchanged -'modules/nf-core/picard/collecthsmetrics/meta.yml' is unchanged -Changes in 'picard/collecthsmetrics/main.nf': ---- modules/nf-core/picard/collecthsmetrics/main.nf -+++ modules/nf-core/picard/collecthsmetrics/main.nf -@@ -8,11 +8,7 @@ - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: -- tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') -- tuple val(meta2), path(ref) -- tuple val(meta3), path(ref_fai) -- tuple val(meta4), path(ref_dict) -- tuple val(meta5), path(ref_gzi) -+ tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "bait/*"), path(target_intervals, stageAs: "target/*") ,path(fasta) ,path(fai) ,path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics -@@ -24,7 +20,7 @@ - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" -- def reference = ref ? "--REFERENCE_SEQUENCE ${ref}" : "" -+ def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - - def avail_mem = 3072 - if (!task.memory) { -@@ -38,16 +34,17 @@ - def bait_intervallist_cmd = "" - if (bait_intervals =~ /.(bed|bed.gz)$/) { - bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") -- bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." -+ bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - - def target_interval_list = target_intervals - def target_intervallist_cmd = "" - if (target_intervals =~ /.(bed|bed.gz)$/) { - target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") -- target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." -+ target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." - } - """ -+ export TMP=\$PWD - ${bait_intervallist_cmd} - ${target_intervallist_cmd} - -@@ -59,7 +56,8 @@ - --BAIT_INTERVALS ${bait_interval_list} \\ - --TARGET_INTERVALS ${target_interval_list} \\ - --INPUT ${bam} \\ -- --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics -+ --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics \\ -+ --TMP_DIR . - """ - - stub: - -'modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap' is unchanged -'modules/nf-core/picard/collecthsmetrics/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test deleted file mode 100644 index d7366111..00000000 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ /dev/null @@ -1,221 +0,0 @@ -nextflow_process { - - name "Test Process PICARD_COLLECTHSMETRICS" - script "../main.nf" - process "PICARD_COLLECTHSMETRICS" - - tag "modules" - tag "modules_nfcore" - tag "picard" - tag "picard/collecthsmetrics" - - test("sarscov2 - bam") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - gzippedfa") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.gzi', checkIfExists: true)] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("sarscov2 - bam - nofasta") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) - ] - input[1] = [[:],[]] - input[2] = [[:],[]] - input[3] = [[:],[]] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - bed") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) - ] - - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sarscov2 - bam - samebed") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true) - ] - - input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] - input[4] = [[:],[]] - """ - } - } - - then { - def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..100] - lines.remove(3) // remove timestamp - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).name, - size, - lines, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } -} diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap deleted file mode 100644 index 43385314..00000000 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ /dev/null @@ -1,639 +0,0 @@ -{ - "sarscov2 - bam - nofasta": { - "content": [ - "test.CollectHsMetrics.coverage_metrics", - 3548, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - "37\t0\t0", - "38\t0\t0", - "39\t0\t0", - "40\t0\t0", - "41\t0\t0", - "42\t0\t0", - "43\t0\t0", - "44\t0\t0", - "45\t0\t0", - "46\t0\t0", - "47\t0\t0", - "48\t0\t0", - "49\t0\t0", - "50\t0\t0", - "51\t0\t0", - "52\t0\t0", - "53\t0\t0", - "54\t0\t0", - "55\t0\t0", - "56\t0\t0", - "57\t0\t0", - "58\t0\t0", - "59\t0\t0", - "60\t0\t0", - "61\t0\t0", - "62\t0\t0", - "63\t0\t0", - "64\t0\t0", - "65\t0\t0", - "66\t0\t0", - "67\t0\t0", - "68\t0\t0", - "69\t0\t0", - "70\t0\t0", - "71\t0\t0", - "72\t0\t0", - "73\t0\t0", - "74\t0\t0", - "75\t0\t0", - "76\t0\t0", - "77\t0\t0", - "78\t0\t0", - "79\t0\t0", - "80\t0\t0", - "81\t0\t0", - "82\t0\t0", - "83\t0\t0", - "84\t0\t0", - "85\t0\t0", - "86\t0\t0", - "87\t0\t0", - "88\t0\t0", - "89\t0\t0" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-01-05T17:03:29.566021877", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "sarscov2 - bam - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-19T17:36:03.822502867", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "sarscov2 - bam - gzippedfa": { - "content": [ - "test.CollectHsMetrics.coverage_metrics", - 3601, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta.gz --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - "37\t0\t0", - "38\t0\t0", - "39\t0\t0", - "40\t0\t0", - "41\t0\t0", - "42\t0\t0", - "43\t0\t0", - "44\t0\t0", - "45\t0\t0", - "46\t0\t0", - "47\t0\t0", - "48\t0\t0", - "49\t0\t0", - "50\t0\t0", - "51\t0\t0", - "52\t0\t0", - "53\t0\t0", - "54\t0\t0", - "55\t0\t0", - "56\t0\t0", - "57\t0\t0", - "58\t0\t0", - "59\t0\t0", - "60\t0\t0", - "61\t0\t0", - "62\t0\t0", - "63\t0\t0", - "64\t0\t0", - "65\t0\t0", - "66\t0\t0", - "67\t0\t0", - "68\t0\t0", - "69\t0\t0", - "70\t0\t0", - "71\t0\t0", - "72\t0\t0", - "73\t0\t0", - "74\t0\t0", - "75\t0\t0", - "76\t0\t0", - "77\t0\t0", - "78\t0\t0", - "79\t0\t0", - "80\t0\t0", - "81\t0\t0", - "82\t0\t0", - "83\t0\t0", - "84\t0\t0", - "85\t0\t0", - "86\t0\t0", - "87\t0\t0", - "88\t0\t0", - "89\t0\t0" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-01-05T17:03:04.382110367", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "sarscov2 - bam - samebed": { - "content": [ - "test.CollectHsMetrics.coverage_metrics", - 3586, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/baits.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394337\t2\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t0\t0", - "1\t0\t0", - "2\t93\t0", - "3\t65\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t28", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t9", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t20", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t90", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t262", - 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3598, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - 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"test.CollectHsMetrics.coverage_metrics", - 3595, - [ - "## htsjdk.samtools.metrics.StringHeader", - "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/test.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", - "## htsjdk.samtools.metrics.StringHeader", - "", - "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", - "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", - "", - "## HISTOGRAM\tjava.lang.Integer", - "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", - "0\t89\t0", - "1\t5\t0", - "2\t0\t0", - "3\t0\t0", - "4\t0\t0", - "5\t0\t0", - "6\t0\t0", - "7\t0\t0", - "8\t0\t0", - "9\t0\t0", - "10\t0\t0", - "11\t0\t0", - "12\t0\t0", - "13\t0\t0", - "14\t0\t5", - "15\t0\t0", - "16\t0\t0", - "17\t0\t0", - "18\t0\t0", - "19\t0\t0", - "20\t0\t0", - "21\t0\t1", - "22\t0\t0", - "23\t0\t0", - "24\t0\t0", - "25\t0\t0", - "26\t0\t0", - "27\t0\t0", - "28\t0\t0", - "29\t0\t0", - "30\t0\t0", - "31\t0\t0", - "32\t0\t1", - "33\t0\t0", - "34\t0\t0", - "35\t0\t0", - "36\t0\t3", - 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tag "${meta.id}" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: - tuple val(meta) , path(bam), path(bai), path(intervals), path(fasta) ,path(fai), path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics - tuple val(meta), path("*.pdf"), emit: pdf, optional: true - tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def intervals_cmd = intervals ? "--INTERVALS ${intervals.join(',')}" : "" - def reference_cmd = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - def avail_mem = 3072 - if (!task.memory) { - log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') - } - else { - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ - export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectMultipleMetrics \\ - ${args} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectMultipleMetrics \\ - --TMP_DIR . \\ - ${reference_cmd} \\ - ${intervals_cmd} - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics - touch ${prefix}.CollectMultipleMetrics.insert_size_metrics - touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf - touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics - touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics - touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf - touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf - touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf - touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf - touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics - """ -} diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml deleted file mode 100644 index 213d600b..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ /dev/null @@ -1,103 +0,0 @@ -name: picard_collectmultiplemetrics -description: Collect multiple metrics from a BAM file -keywords: - - alignment - - metrics - - statistics - - insert - - quality - - bam -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ["MIT"] - identifier: biotools:picard_tools -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: SAM/BAM/CRAM file - pattern: "*.{sam,bam,cram}" - ontologies: [] - - bai: - type: file - description: Optional SAM/BAM/CRAM file index - pattern: "*.{sai,bai,crai}" - ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fasta: - type: file - description: Genome fasta file - ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fai: - type: file - description: Index of FASTA file. Only needed when fasta is supplied. - pattern: "*.fai" - ontologies: [] -output: - metrics: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*_metrics": - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - ontologies: [] - pdf: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.pdf": - type: file - description: PDF plots of metrics - pattern: "*.{pdf}" - ontologies: [] - versions_picard: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool - -authors: - - "@drpatelh" -maintainers: - - "@drpatelh" diff --git a/modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff b/modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff deleted file mode 100644 index 780c0862..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff +++ /dev/null @@ -1,49 +0,0 @@ -Changes in component 'nf-core/picard/collectmultiplemetrics' -'modules/nf-core/picard/collectmultiplemetrics/environment.yml' is unchanged -'modules/nf-core/picard/collectmultiplemetrics/meta.yml' is unchanged -Changes in 'picard/collectmultiplemetrics/main.nf': ---- modules/nf-core/picard/collectmultiplemetrics/main.nf -+++ modules/nf-core/picard/collectmultiplemetrics/main.nf -@@ -8,9 +8,7 @@ - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: -- tuple val(meta), path(bam), path(bai) -- tuple val(meta2), path(fasta) -- tuple val(meta3), path(fai) -+ tuple val(meta) , path(bam), path(bai), path(intervals), path(fasta) ,path(fai), path(dict) - - output: - tuple val(meta), path("*_metrics"), emit: metrics -@@ -23,7 +21,8 @@ - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" -- def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" -+ def intervals_cmd = intervals ? "--INTERVALS ${intervals.join(',')}" : "" -+ def reference_cmd = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - def avail_mem = 3072 - if (!task.memory) { - log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') -@@ -32,13 +31,16 @@ - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ -+ export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectMultipleMetrics \\ - ${args} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectMultipleMetrics \\ -- ${reference} -+ --TMP_DIR . \\ -+ ${reference_cmd} \\ -+ ${intervals_cmd} - """ - - stub: - -'modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap' is unchanged -'modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test deleted file mode 100644 index 0037acab..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test +++ /dev/null @@ -1,186 +0,0 @@ - -nextflow_process { - - name "Test Process PICARD_COLLECTMULTIPLEMETRICS" - script "../main.nf" - process "PICARD_COLLECTMULTIPLEMETRICS" - - tag "modules" - tag "modules_nfcore" - tag "picard" - tag "picard/collectmultiplemetrics" - - test("test-picard-collectmultiplemetrics") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.metrics[0][1].collect { file(it).name }.toSorted(), - process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectmultiplemetrics-nofasta") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [[id:'genome'],[]] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.metrics[0][1].collect { file(it).name }.toSorted(), - process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectmultiplemetrics-cram") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.metrics[0][1].collect { file(it).name }.toSorted(), - process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectmultiplemetrics - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("test-picard-collectmultiplemetrics-nofasta - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [[id:'genome'],[]] - input[2] = [[id:'genome'],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("test-picard-collectmultiplemetrics-cram - stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } -} diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap deleted file mode 100644 index 393ed100..00000000 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ /dev/null @@ -1,242 +0,0 @@ -{ - "test-picard-collectmultiplemetrics": { - "content": [ - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ], - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-02T10:22:21.230301646", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "test-picard-collectmultiplemetrics - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "pdf": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:32:38.701455244", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectmultiplemetrics-nofasta - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "pdf": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:32:48.923918624", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectmultiplemetrics-cram": { - "content": [ - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ], - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-02T10:23:52.23446844", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "test-picard-collectmultiplemetrics-nofasta": { - "content": [ - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ], - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ], - { - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-02T10:23:27.387621193", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - } - }, - "test-picard-collectmultiplemetrics-cram - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "pdf": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTMULTIPLEMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:32:57.11686549", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf deleted file mode 100644 index 538f77be..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ /dev/null @@ -1,51 +0,0 @@ -process PICARD_COLLECTWGSMETRICS { - tag "${meta.id}" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: - tuple val(meta), path(bam), path(bai) ,path(fasta) ,path(fai), path(dict) - path intervallist - - output: - tuple val(meta), path("*_metrics"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3072 - def interval = intervallist ? "--INTERVALS ${intervallist}" : '' - if (!task.memory) { - log.info('[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') - } - else { - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ - export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectWgsMetrics \\ - ${args} \\ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ - --REFERENCE_SEQUENCE ${fasta} \\ - --TMP_DIR . \\ - ${interval} - - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.CollectWgsMetrics.coverage_metrics - """ -} diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml deleted file mode 100644 index c5afe2e7..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ /dev/null @@ -1,102 +0,0 @@ -name: picard_collectwgsmetrics -description: Collect metrics about coverage and performance of whole genome sequencing - (WGS) experiments. -keywords: - - alignment - - metrics - - statistics - - quality - - bam -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ["MIT"] - identifier: biotools:picard_tools -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Aligned reads file - pattern: "*.{bam, cram}" - ontologies: [] - - bai: - type: file - description: (Optional) Aligned reads file index - pattern: "*.{bai,crai}" - ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta,fna}" - ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome fasta file index - pattern: "*.{fai}" - ontologies: [] - - intervallist: - type: file - description: Picard Interval List. Defines which contigs to include. Can be generated - from a BED file with GATK BedToIntervalList. - ontologies: [] -output: - metrics: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*_metrics": - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - ontologies: [] - versions_picard: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - picard: - type: string - description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": - type: string - description: The command used to generate the version of the tool -authors: - - "@drpatelh" - - "@flowuenne" - - "@lassefolkersen" - - "@ramprasadn" -maintainers: - - "@drpatelh" - - "@flowuenne" - - "@lassefolkersen" - - "@ramprasadn" diff --git a/modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff b/modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff deleted file mode 100644 index 5de262d0..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff +++ /dev/null @@ -1,41 +0,0 @@ -Changes in component 'nf-core/picard/collectwgsmetrics' -'modules/nf-core/picard/collectwgsmetrics/environment.yml' is unchanged -'modules/nf-core/picard/collectwgsmetrics/meta.yml' is unchanged -Changes in 'picard/collectwgsmetrics/main.nf': ---- modules/nf-core/picard/collectwgsmetrics/main.nf -+++ modules/nf-core/picard/collectwgsmetrics/main.nf -@@ -8,10 +8,8 @@ - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" - - input: -- tuple val(meta), path(bam), path(bai) -- tuple val(meta2), path(fasta) -- tuple val(meta3), path(fai) -- path intervallist -+ tuple val(meta), path(bam), path(bai) ,path(fasta) ,path(fai), path(dict) -+ path intervallist - - output: - tuple val(meta), path("*_metrics"), emit: metrics -@@ -32,6 +30,7 @@ - avail_mem = (task.memory.mega * 0.8).intValue() - } - """ -+ export TMP=\$PWD - picard \\ - -Xmx${avail_mem}M \\ - CollectWgsMetrics \\ -@@ -39,7 +38,9 @@ - --INPUT ${bam} \\ - --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ - --REFERENCE_SEQUENCE ${fasta} \\ -+ --TMP_DIR . \\ - ${interval} -+ - """ - - stub: - -'modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap' is unchanged -'modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test deleted file mode 100644 index 1bda5980..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test +++ /dev/null @@ -1,138 +0,0 @@ - -nextflow_process { - - name "Test Process PICARD_COLLECTWGSMETRICS" - script "../main.nf" - process "PICARD_COLLECTWGSMETRICS" - - tag "modules" - tag "modules_nfcore" - tag "picard" - tag "picard/collectwgsmetrics" - - test("test-picard-collectwgsmetrics") { - - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectwgsmetrics-with-interval") { - - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - [] - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("test-picard-collectwgsmetrics - stub") { - options "-stub" - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } - - test("test-picard-collectwgsmetrics-with-interval - stub") { - options "-stub" - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - [] - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } -} diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap deleted file mode 100644 index 79f1145f..00000000 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ /dev/null @@ -1,94 +0,0 @@ -{ - "test-picard-collectwgsmetrics-with-interval - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:35:04.636691319", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectwgsmetrics-with-interval": { - "content": [ - false, - { - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:34:45.059411647", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectwgsmetrics - stub": { - "content": [ - { - "metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:34:54.347278951", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test-picard-collectwgsmetrics": { - "content": [ - false, - { - "versions_picard": [ - [ - "PICARD_COLLECTWGSMETRICS", - "picard", - "3.4.0" - ] - ] - } - ], - "timestamp": "2026-02-20T10:34:25.744978033", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file diff --git a/modules/nf-core/riker/multi/environment.yml b/modules/nf-core/riker/multi/environment.yml new file mode 100644 index 00000000..26cbc6c3 --- /dev/null +++ b/modules/nf-core/riker/multi/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::riker=0.4.0 diff --git a/modules/nf-core/riker/multi/main.nf b/modules/nf-core/riker/multi/main.nf new file mode 100644 index 00000000..e557e754 --- /dev/null +++ b/modules/nf-core/riker/multi/main.nf @@ -0,0 +1,97 @@ +process RIKER_MULTI { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/54c7820b49cfb5fada32c1825ac8a46c05d0085105c50055cbce4c37701ab95e/data' : + 'community.wave.seqera.io/library/riker:0.4.0--4e7eeb0beed906c0' }" + + input: + tuple val(meta), path(bam), path(bai), path(error_vcf), path(error_vcf_idx), path(error_intervals), path(gcbias_exclude_intervals), path(hybcap_baits, stageAs: 'baits/*'), path(hybcap_targets, stageAs: 'targets/*'), path(rna_gene_model), path(rna_ribosomal_intervals), path(wgs_intervals), path(fasta), path(fai) + + output: + tuple val(meta), path("*.alignment-metrics.txt"), emit: alignment_metrics, optional: true + tuple val(meta), path("*.base-distribution-by-cycle.txt"), emit: base_dist, optional: true + tuple val(meta), path("*.error-indel.txt"), emit: error_indel, optional: true + tuple val(meta), path("*.error-mismatch.txt"), emit: error_mismatch, optional: true + tuple val(meta), path("*.error-overlap.txt"), emit: error_overlap, optional: true + tuple val(meta), path("*.gcbias-detail.txt"), emit: gcbias_detail, optional: true + tuple val(meta), path("*.gcbias-summary.txt"), emit: gcbias_summary, optional: true + tuple val(meta), path("*.hybcap-metrics.txt"), emit: hybcap_metrics, optional: true + tuple val(meta), path("*.hybcap-per-base.txt*"), emit: hybcap_per_base, optional: true + tuple val(meta), path("*.hybcap-per-target.txt"), emit: hybcap_per_target, optional: true + tuple val(meta), path("*.isize-histogram.txt"), emit: isize_histogram, optional: true + tuple val(meta), path("*.isize-metrics.txt"), emit: isize_metrics, optional: true + tuple val(meta), path("*.mean-quality-by-cycle.txt"), emit: mean_qual, optional: true + tuple val(meta), path("*.pdf"), emit: pdf, optional: true + tuple val(meta), path("*.quality-score-distribution.txt"), emit: qual_dist, optional: true + tuple val(meta), path("*.rna-biotype.txt"), emit: rna_biotype, optional: true + tuple val(meta), path("*.rna-insert-size-histogram.txt"), emit: rna_insert_size_histogram, optional: true + tuple val(meta), path("*.rna-insert-size.txt"), emit: rna_insert_size, optional: true + tuple val(meta), path("*.rna-metrics.txt"), emit: rna_metrics, optional: true + tuple val(meta), path("*.wgs-coverage.txt"), emit: wgs_coverage, optional: true + tuple val(meta), path("*.wgs-metrics.txt"), emit: wgs_metrics, optional: true + tuple val("${task.process}"), val('riker'), eval("riker --version 2>&1 | sed 's/riker //'") , topic: versions, emit: versions_riker + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference_arg = fasta ? "--reference ${fasta}" : '' + if ((hybcap_baits as Boolean) ^ (hybcap_targets as Boolean)) { + error "RIKER_MULTI: both 'baits' and 'targets' must be provided together, or neither" + } + def error_vcf_arg = error_vcf && error_vcf_idx ? "--error::vcf ${error_vcf}" : '' + def error_intervals_arg = error_intervals ? "--error::intervals ${error_intervals}" : '' + def gcbias_exclude_intervals_arg = gcbias_exclude_intervals ? "--gcbias::exclude-intervals ${gcbias_exclude_intervals}" : '' + def hybcap_opts = (hybcap_baits && hybcap_targets) ? "--hybcap::baits ${hybcap_baits} --hybcap::targets ${hybcap_targets}" : '' + def rna_gene_model_arg = rna_gene_model ? "--rna::gene-model ${rna_gene_model}" : '' + def rna_ribosomal_intervals_arg = rna_ribosomal_intervals ? "--rna::ribosomal-intervals ${rna_ribosomal_intervals}" : '' + def wgs_intervals_arg = wgs_intervals ? "--wgs::intervals ${wgs_intervals}" : '' + + """ + riker multi \\ + -i ${bam} \\ + ${reference_arg} \\ + -o ${prefix} \\ + --threads ${task.cpus} \\ + ${hybcap_opts} \\ + ${error_vcf_arg} \\ + ${error_intervals_arg} \\ + ${gcbias_exclude_intervals_arg} \\ + ${rna_gene_model_arg} \\ + ${rna_ribosomal_intervals_arg} \\ + ${wgs_intervals_arg} \\ + ${args} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.alignment-metrics.txt + touch ${prefix}.base-distribution-by-cycle.txt + touch ${prefix}.mean-quality-by-cycle.txt + touch ${prefix}.quality-score-distribution.txt + touch ${prefix}.error-mismatch.txt + touch ${prefix}.error-overlap.txt + touch ${prefix}.error-indel.txt + touch ${prefix}.gcbias-detail.txt + touch ${prefix}.gcbias-summary.txt + touch ${prefix}.hybcap-metrics.txt + touch ${prefix}.hybcap-per-target.txt + touch ${prefix}.hybcap-per-base.txt + touch ${prefix}.isize-metrics.txt + touch ${prefix}.isize-histogram.txt + touch ${prefix}.wgs-metrics.txt + touch ${prefix}.wgs-coverage.txt + touch ${prefix}.base-distribution-by-cycle.pdf + touch ${prefix}.gcbias-chart.pdf + touch ${prefix}.isize-histogram.pdf + touch ${prefix}.mean-quality-by-cycle.pdf + touch ${prefix}.quality-score-distribution.pdf + touch ${prefix}.wgs-coverage.pdf + """ +} diff --git a/modules/nf-core/riker/multi/meta.yml b/modules/nf-core/riker/multi/meta.yml new file mode 100644 index 00000000..89897d6c --- /dev/null +++ b/modules/nf-core/riker/multi/meta.yml @@ -0,0 +1,354 @@ +name: riker_multi +description: | + Run multiple riker collectors in a single BAM pass using riker multi. Specify + tools via ext.args (e.g. '--tools alignment basic isize'). The wgs, gcbias, and + error tools require a reference FASTA; the hybcap tool requires baits and targets. +keywords: + - bam + - qc + - metrics + - multi + - alignment + - insert size + - gc bias + - coverage + - rna +tools: + - riker: + description: | + Fast Rust CLI toolkit for sequencing QC metrics. Ports key QC metrics tools + from Picard with cleaner output and better performance. + homepage: https://github.com/fulcrumgenomics/riker + documentation: https://github.com/fulcrumgenomics/riker + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Aligned reads in BAM, CRAM, or SAM format + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_2572" # BAM + - edam: "http://edamontology.org/format_3462" # CRAM + - bai: + type: file + description: Index for the BAM/CRAM file + pattern: "*.{bai,crai}" + ontologies: + - edam: "http://edamontology.org/format_3327" # BAI + - error_vcf: + type: file + description: VCF file containing known variants for error metrics. Must be bgzipped and indexed. + pattern: "*.vcf.gz" + ontologies: + - edam: "http://edamontology.org/format_3016" # VCF + - error_vcf_idx: + type: file + description: Index for the VCF file. + pattern: "*.vcf.gz.{tbi,csi}" + ontologies: + - edam: "http://edamontology.org/format_3616" # TBI/CSI + - error_intervals: + type: file + description: IntervalList or BED file containing regions to exclude from error metrics. Optional. + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - gcbias_exclude_intervals: + type: file + description: IntervalList or BED file containing regions to exclude from GC bias metrics. Optional. + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - hybcap_baits: + type: file + description: Bait interval file (IntervalList or BED). Required when running the hybcap tool. Optional otherwise. + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - hybcap_targets: + type: file + description: Target interval file (IntervalList or BED). Required when running the hybcap tool. Optional otherwise. + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - rna_gene_model: + type: file + description: GTF or GFF file containing gene models. Required when running the rna tool. Optional otherwise. + pattern: "*.{gtf,gff}" + ontologies: + - edam: "http://edamontology.org/format_2306" # GTF + - edam: "http://edamontology.org/format_1975" # GFF + - rna_ribosomal_intervals: + type: file + description: Explicit ribosomal intervals (BED or Picard IntervalList), unioned with biotype-derived rRNA genes from the gene model + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - wgs_intervals: + type: file + description: IntervalList or BED file containing intervals for whole-genome coverage metrics. Required when running the wgs tool. Optional otherwise. + pattern: "*.{interval_list,bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file. Required when running wgs, gcbias, or error tools. + pattern: "*.{fa,fasta,fna}" + ontologies: + - edam: "http://edamontology.org/format_1929" # FASTA + - fai: + type: file + description: Index for the reference FASTA file + pattern: "*.fai" + ontologies: + - edam: "http://edamontology.org/format_3326" # FASTA index +output: + alignment_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.alignment-metrics.txt": + type: file + description: Alignment summary metrics (alignment tool) + pattern: "*.alignment-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + base_dist: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.base-distribution-by-cycle.txt": + type: file + description: Base distribution by cycle (basic tool) + pattern: "*.base-distribution-by-cycle.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + error_indel: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.error-indel.txt": + type: file + description: Indel error metrics (error tool) + pattern: "*.error-indel.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + error_mismatch: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.error-mismatch.txt": + type: file + description: Base mismatch error metrics (error tool) + pattern: "*.error-mismatch.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + error_overlap: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.error-overlap.txt": + type: file + description: Read overlap error metrics (error tool) + pattern: "*.error-overlap.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + gcbias_detail: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.gcbias-detail.txt": + type: file + description: Per-GC-bin detail metrics (gcbias tool) + pattern: "*.gcbias-detail.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + gcbias_summary: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.gcbias-summary.txt": + type: file + description: GC bias summary metrics (gcbias tool) + pattern: "*.gcbias-summary.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + hybcap_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.hybcap-metrics.txt": + type: file + description: Hybrid capture summary metrics (hybcap tool) + pattern: "*.hybcap-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + hybcap_per_base: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.hybcap-per-base.txt*": + type: file + description: Per-base coverage values (hybcap tool, optional) + pattern: "*.hybcap-per-base.txt{,.gz}" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + hybcap_per_target: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.hybcap-per-target.txt": + type: file + description: Per-target coverage metrics (hybcap tool, optional) + pattern: "*.hybcap-per-target.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + isize_histogram: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.isize-histogram.txt": + type: file + description: Insert size histogram (isize tool) + pattern: "*.isize-histogram.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + isize_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.isize-metrics.txt": + type: file + description: Insert size summary metrics (isize tool) + pattern: "*.isize-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + mean_qual: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.mean-quality-by-cycle.txt": + type: file + description: Mean quality by cycle (basic tool) + pattern: "*.mean-quality-by-cycle.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + pdf: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.pdf": + type: file + description: PDF plots from any tool that generates them + pattern: "*.pdf" + ontologies: + - edam: "http://edamontology.org/format_3508" # PDF + qual_dist: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.quality-score-distribution.txt": + type: file + description: Quality score distribution (basic tool) + pattern: "*.quality-score-distribution.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + rna_biotype: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.rna-biotype.txt": + type: file + description: RNA biotype metrics (rna tool) + pattern: "*.rna-biotype.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + rna_insert_size_histogram: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.rna-insert-size-histogram.txt": + type: file + description: RNA insert size histogram (rna tool) + pattern: "*.rna-insert-size-histogram.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + rna_insert_size: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.rna-insert-size.txt": + type: file + description: RNA insert size metrics (rna tool) + pattern: "*.rna-insert-size.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + rna_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.rna-metrics.txt": + type: file + description: RNA summary metrics (rna tool) + pattern: "*.rna-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + wgs_coverage: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.wgs-coverage.txt": + type: file + description: Per-depth coverage histogram (wgs tool) + pattern: "*.wgs-coverage.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + wgs_metrics: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.wgs-metrics.txt": + type: file + description: Whole-genome coverage summary metrics (wgs tool) + pattern: "*.wgs-metrics.txt" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + versions_riker: + - - ${task.process}: + type: string + description: The name of the process + - riker: + type: string + description: The name of the tool + - riker --version 2>&1 | sed 's/riker //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - riker: + type: string + description: The name of the tool + - riker --version 2>&1 | sed 's/riker //': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@emmcauley" + - "@matthdsm" + - "@tfenne" +maintainers: + - "@emmcauley" + - "@matthdsm" diff --git a/modules/nf-core/riker/multi/riker-multi.diff b/modules/nf-core/riker/multi/riker-multi.diff new file mode 100644 index 00000000..ca626a12 --- /dev/null +++ b/modules/nf-core/riker/multi/riker-multi.diff @@ -0,0 +1,21 @@ +Changes in component 'nf-core/riker/multi' +'modules/nf-core/riker/multi/environment.yml' is unchanged +'modules/nf-core/riker/multi/meta.yml' is unchanged +Changes in 'riker/multi/main.nf': +--- modules/nf-core/riker/multi/main.nf ++++ modules/nf-core/riker/multi/main.nf +@@ -8,8 +8,7 @@ + 'community.wave.seqera.io/library/riker:0.4.0--4e7eeb0beed906c0' }" + + input: +- tuple val(meta), path(bam), path(bai), path(error_vcf), path(error_vcf_idx), path(error_intervals), path(gcbias_exclude_intervals), path(hybcap_baits, stageAs: 'baits/*'), path(hybcap_targets, stageAs: 'targets/*'), path(rna_gene_model), path(rna_ribosomal_intervals), path(wgs_intervals) +- tuple val(meta2), path(fasta), path(fai) ++ tuple val(meta), path(bam), path(bai), path(error_vcf), path(error_vcf_idx), path(error_intervals), path(gcbias_exclude_intervals), path(hybcap_baits, stageAs: 'baits/*'), path(hybcap_targets, stageAs: 'targets/*'), path(rna_gene_model), path(rna_ribosomal_intervals), path(wgs_intervals), path(fasta), path(fai) + + output: + tuple val(meta), path("*.alignment-metrics.txt"), emit: alignment_metrics, optional: true + +'modules/nf-core/riker/multi/tests/main.nf.test.snap' is unchanged +'modules/nf-core/riker/multi/tests/nextflow.config' is unchanged +'modules/nf-core/riker/multi/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/riker/multi/tests/main.nf.test b/modules/nf-core/riker/multi/tests/main.nf.test new file mode 100644 index 00000000..3b7b6db0 --- /dev/null +++ b/modules/nf-core/riker/multi/tests/main.nf.test @@ -0,0 +1,454 @@ +nextflow_process { + + name "Test Process RIKER_MULTI" + script "../main.nf" + process "RIKER_MULTI" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "riker" + tag "riker/multi" + + test("sarscov2 - paired_end - bam - alignment basic isize") { + + when { + params { + module_args = '--tools alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), // bam + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), // bai + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - wgs gcbias") { + + when { + params { + module_args = '--tools wgs gcbias' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - wgs gcbias alignment basic isize") { + + when { + params { + module_args = '--tools wgs gcbias alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("homo_sapiens - paired_end - cram - alignment basic isize") { + + when { + params { + module_args = '--tools alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - hybcap") { + + when { + params { + module_args = '--tools hybcap' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), // hybcap_baits + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true), // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - error") { + + when { + params { + module_args = '--tools error --error::stratify-by bq isize gc' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - error alignment") { + + when { + params { + module_args = '--tools error alignment --error::stratify-by bq isize gc' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - all tools") { + + when { + params { + module_args = '--tools alignment basic isize wgs gcbias hybcap error --error::stratify-by bq isize gc' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true), + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - baits without targets fails") { + + when { + params { + module_args = '--tools hybcap' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assert process.failed + } + } + + test("sarscov2 - paired_end - bam - targets without baits fails") { + + when { + params { + module_args = '--tools hybcap' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true), + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assert process.failed + } + } + + test("homo_sapiens - paired_end - bam - rna") { + when { + params { + module_args = '--tools rna' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gff3', checkIfExists: true), + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["pdf","rna_biotype","rna_insert_size_histogram"])).match() } + ) + } + } + + test("sarscov2 - paired_end - bam - stub") { + + options "-stub" + + when { + params { + module_args = '--tools alignment basic isize' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], // error_vcf + [], // error_vcf_idx + [], // error_intervals + [], // gcbias_exclude_intervals + [], // hybcap_baits + [], // hybcap_targets + [], // rna_gene_model + [], // rna_ribosomal_intervals + [] // wgs_intervals + ] + input[1] = [[],[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/riker/multi/tests/main.nf.test.snap b/modules/nf-core/riker/multi/tests/main.nf.test.snap new file mode 100644 index 00000000..8fafc3b9 --- /dev/null +++ b/modules/nf-core/riker/multi/tests/main.nf.test.snap @@ -0,0 +1,1475 @@ +{ + "sarscov2 - paired_end - bam - alignment basic isize": { + "content": [ + { + "alignment_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.alignment-metrics.txt:md5,ef2421780f4e1127dac0ae3d6702d33f" + ] + ], + "base_dist": [ + [ + { + "id": "test", + "single_end": false + }, + "test.base-distribution-by-cycle.txt:md5,921d4ed3fc1ddb54b8e7c616d78e0736" + ] + ], + "error_indel": [ + + ], + "error_mismatch": [ + + ], + "error_overlap": [ + + ], + "gcbias_detail": [ + + ], + "gcbias_summary": [ + + ], + "hybcap_metrics": [ + + ], + "hybcap_per_base": [ + + ], + "hybcap_per_target": [ + + ], + "isize_histogram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.isize-histogram.txt:md5,68742e205c83b880802c3c5bbe7e882c" + ] + ], + "isize_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.isize-metrics.txt:md5,c3bef6653b685c99e373a1dfccedc52d" + ] + ], + "mean_qual": [ + [ + { + "id": "test", + "single_end": false + }, + "test.mean-quality-by-cycle.txt:md5,476932952a367fe567eba75d6ff51630" + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.base-distribution-by-cycle.pdf", + "test.isize-histogram.pdf", + "test.mean-quality-by-cycle.pdf", + "test.quality-score-distribution.pdf" + ] + ] + ], + "qual_dist": [ + [ + { + "id": "test", + "single_end": false + }, + "test.quality-score-distribution.txt:md5,d5f17682727e31f05dc8b29b7c06b3ab" + ] + ], + "rna_biotype": [ + + ], + "rna_insert_size": [ + + ], + "rna_insert_size_histogram": [ + + ], + "rna_metrics": [ + + ], + "versions_riker": [ + [ + "RIKER_MULTI", + "riker", + "0.4.0" + ] + ], + "wgs_coverage": [ + 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"2026-07-07T09:26:15.635157", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } + }, + "sarscov2 - paired_end - bam - wgs gcbias": { + "content": [ + { + "alignment_metrics": [ + + ], + "base_dist": [ + + ], + "error_indel": [ + + ], + "error_mismatch": [ + + ], + "error_overlap": [ + + ], + "gcbias_detail": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gcbias-detail.txt:md5,44cd58d1a0bd81ca8ea5d3fa7c07e4db" + ] + ], + "gcbias_summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gcbias-summary.txt:md5,4915d05211aaae398fc0f29ab3cc79b8" + ] + ], + "hybcap_metrics": [ + + ], + "hybcap_per_base": [ + + ], + "hybcap_per_target": [ + + ], + "isize_histogram": [ + + ], + "isize_metrics": [ + + ], + "mean_qual": [ + + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.gcbias-chart.pdf", + "test.wgs-coverage.pdf" + ] + ] + ], + "qual_dist": [ + + ], + "rna_biotype": [ + + ], + "rna_insert_size": [ + + ], + "rna_insert_size_histogram": [ + + ], + "rna_metrics": [ + + ], + "versions_riker": [ + [ + "RIKER_MULTI", + "riker", + "0.4.0" + ] + ], + "wgs_coverage": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wgs-coverage.txt:md5,8fd648b0045ff06fc3ba46772e33255c" + ] + ], + "wgs_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wgs-metrics.txt:md5,d7bb5636d4abeefe85f5ca2a6674adb2" + ] + ] + } + ], + "timestamp": "2026-07-07T09:25:50.544718", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/riker/multi/tests/nextflow.config b/modules/nf-core/riker/multi/tests/nextflow.config new file mode 100644 index 00000000..83152a66 --- /dev/null +++ b/modules/nf-core/riker/multi/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'RIKER_MULTI' { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index 946bb362..6a19f168 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.24 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.24 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index f4afd726..5c92969a 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONVERT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.24--d697cfb9dce007cd'}" input: tuple val(meta), path(input), path(index), path(fasta), path(fai) diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test b/modules/nf-core/samtools/convert/tests/main.nf.test index 638caabe..a4848662 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test +++ b/modules/nf-core/samtools/convert/tests/main.nf.test @@ -30,11 +30,13 @@ nextflow_process { then { assert process.success - assert snapshot( - process.out.cram.collect{ meta, cram_file -> [ meta, file(cram_file).name] }, - process.out.crai.collect{ meta, crai_file -> [ meta, file(crai_file).name] }, - ["versions_samtools": process.out.versions_samtools] - ).match() + assertAll( + { assert snapshot( + process.out.cram.collect{ meta, cram_file -> [ meta, file(cram_file).name] }, + process.out.crai.collect{ meta, crai_file -> [ meta, file(crai_file).name] }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) } } @@ -59,11 +61,13 @@ nextflow_process { then { assert process.success - assert snapshot( - process.out.bam.collect{ meta, bam_file -> [ meta, file(bam_file).name, bam(bam_file).getReadsMD5()] }, - process.out.bai.collect{ meta, bai_file -> [ meta, file(bai_file).name] }, - ["versions_samtools": process.out.versions_samtools] - ).match() + assertAll( + { assert snapshot( + process.out.bam.collect{ meta, bam_file -> [ meta, file(bam_file).name, bam(bam_file).getReadsMD5()] }, + process.out.bai.collect{ meta, bai_file -> [ meta, file(bai_file).name] }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) } } @@ -90,7 +94,9 @@ nextflow_process { then { assert process.success - assert snapshot(sanitizeOutput(process.out)).match() + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } + ) } } } diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap index 0f535753..dd23cbb4 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap @@ -22,16 +22,16 @@ [ "SAMTOOLS_CONVERT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T08:55:56.895841", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:55:56.895841" + } }, "homo_sapiens - [cram, crai], [fasta, fai]": { "content": [ @@ -57,16 +57,16 @@ [ "SAMTOOLS_CONVERT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T08:56:03.056799", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:56:03.056799" + } }, "sarscov2 - [bam, bai], [fasta, fai] - stub": { "content": [ @@ -97,15 +97,15 @@ [ "SAMTOOLS_CONVERT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T08:56:09.165934", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:56:09.165934" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index 946bb362..6a19f168 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.24 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.24 diff --git a/modules/nf-core/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf index 3d7023de..f96889f9 100644 --- a/modules/nf-core/samtools/coverage/main.nf +++ b/modules/nf-core/samtools/coverage/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COVERAGE { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.24--d697cfb9dce007cd'}" input: tuple val(meta), path(input), path(input_index), path(fasta), path(fai) @@ -38,5 +38,6 @@ process SAMTOOLS_COVERAGE { def prefix = task.ext.prefix ?: "${meta.id}" """ echo "#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tmeanbaseq\tmeanmapq" > ${prefix}.txt + echo "chr21\t16570000\t16610000\t8741\t39996\t99.9875\t32.4854\t29.6\t59.8" >> ${prefix}.txt """ } diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test b/modules/nf-core/samtools/coverage/tests/main.nf.test index c59ba4f8..23e5397d 100644 --- a/modules/nf-core/samtools/coverage/tests/main.nf.test +++ b/modules/nf-core/samtools/coverage/tests/main.nf.test @@ -25,8 +25,8 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -52,9 +52,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -111,7 +111,7 @@ nextflow_process { } - test("test_samtools_coverage_stub") { + test("test_samtools_coverage - stub") { options "-stub" @@ -133,12 +133,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap index 359a9599..b460093c 100644 --- a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test_samtools_coverage_stub": { + "test_samtools_coverage - stub": { "content": [ { "coverage": [ @@ -7,23 +7,23 @@ { "id": "test" }, - "test.txt:md5,ea885d54c0223dff86e2e44f5bc08374" + "test.txt:md5,5b5fbaf1b8a9645ab2e9d34891ae165a" ] ], "versions_samtools": [ [ "SAMTOOLS_COVERAGE", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-05-21T15:45:07.736128337", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:56:33.66881" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } }, "test_samtools_coverage_bam": { "content": [ @@ -40,35 +40,20 @@ [ "SAMTOOLS_COVERAGE", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T08:56:13.846408", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:56:13.846408" + } }, "test_samtools_coverage_cram": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.txt:md5,ce896534bac51cfcc97e5508ae907e99" - ] - ], - "1": [ - [ - "SAMTOOLS_COVERAGE", - "samtools", - "1.23.1" - ] - ], "coverage": [ [ { @@ -81,15 +66,15 @@ [ "SAMTOOLS_COVERAGE", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T15:50:47.021688859", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:56:19.040435" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 946bb362..6a19f168 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.24 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.24 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 2d9588b9..f4a0b3b3 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.24--d697cfb9dce007cd'}" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index 3b648a37..dbf7c996 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -23,9 +23,9 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -37,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -47,9 +47,9 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index b110c47c..f572957b 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -2,22 +2,6 @@ "BAM - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,67394650dbae96d1a4fcc70484822159" - ] - ], - "1": [ - [ - "SAMTOOLS_FLAGSTAT", - "samtools", - "1.23.1" - ] - ], "flagstat": [ [ { @@ -31,36 +15,20 @@ [ "SAMTOOLS_FLAGSTAT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T15:53:38.552555213", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:59:26.188788" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "BAM": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" - ] - ], - "1": [ - [ - "SAMTOOLS_FLAGSTAT", - "samtools", - "1.23.1" - ] - ], "flagstat": [ [ { @@ -74,15 +42,15 @@ [ "SAMTOOLS_FLAGSTAT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T15:53:33.931611374", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:59:20.212002" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 946bb362..6a19f168 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.24 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.24 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 4d74768a..58d31062 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.24--d697cfb9dce007cd'}" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index c990cd55..cc204d6a 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -23,8 +23,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.idxstats, process.out.findAll { key, val -> key.startsWith('versions') } @@ -34,11 +34,13 @@ nextflow_process { } test("bam - stub") { + options "-stub" + when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -48,12 +50,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.idxstats, process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) } - }} + } +} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index 7bcde2fd..2dba681c 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -15,16 +15,16 @@ [ "SAMTOOLS_IDXSTATS", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T08:59:41.877526", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:59:41.877526" + } }, "bam": { "content": [ @@ -42,15 +42,15 @@ [ "SAMTOOLS_IDXSTATS", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T08:59:34.725514", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:59:34.725514" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sormadup/environment.yml b/modules/nf-core/samtools/sormadup/environment.yml index 946bb362..6a19f168 100644 --- a/modules/nf-core/samtools/sormadup/environment.yml +++ b/modules/nf-core/samtools/sormadup/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.24 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.24 diff --git a/modules/nf-core/samtools/sormadup/main.nf b/modules/nf-core/samtools/sormadup/main.nf index c0a56ee3..1d6765a3 100644 --- a/modules/nf-core/samtools/sormadup/main.nf +++ b/modules/nf-core/samtools/sormadup/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORMADUP { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.24--d697cfb9dce007cd'}" input: tuple val(meta), path(input), path(fasta), path(fai) diff --git a/modules/nf-core/samtools/sormadup/tests/main.nf.test b/modules/nf-core/samtools/sormadup/tests/main.nf.test index f9bc34e5..61e5d178 100644 --- a/modules/nf-core/samtools/sormadup/tests/main.nf.test +++ b/modules/nf-core/samtools/sormadup/tests/main.nf.test @@ -16,7 +16,6 @@ nextflow_process { input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ] input[1] = [ [ id:'fasta' ], @@ -30,7 +29,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -46,7 +45,6 @@ nextflow_process { input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ] input[1] = [ [ id:'fasta' ], @@ -58,15 +56,12 @@ nextflow_process { } then { - assert process.success def fasta = params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta' + assert process.success assertAll( { assert snapshot( - cram( - process.out.cram[0][1], - fasta, - ).getReadsMD5(), + cram(process.out.cram[0][1], fasta).getReadsMD5(), file(process.out.crai[0][1]).name, process.out.metrics, process.out.findAll { key, val -> key.startsWith("versions") } @@ -87,7 +82,6 @@ nextflow_process { input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ] input[1] = [ [ id:'fasta' ], @@ -101,10 +95,8 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap index e774fc12..5ce63333 100644 --- a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap @@ -2,38 +2,6 @@ "sarscov2 - bam - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test" - }, - "test.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - "SAMTOOLS_SORMADUP", - "samtools", - "1.23.1" - ] - ], "bam": [ [ { @@ -63,16 +31,16 @@ [ "SAMTOOLS_SORMADUP", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T16:09:23.851588322", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:03:58.177246" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "sarscov2 - cram": { "content": [ @@ -91,58 +59,26 @@ [ "SAMTOOLS_SORMADUP", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T09:03:52.7035", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:03:52.7035" + } }, "sarscov2 - bam": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.bam:md5,706f3bc699aa89ae43868fcfd38a0d71" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test" - }, - "test.metrics:md5,6093d8853805578a1868f22ff68177e7" - ] - ], - "5": [ - [ - "SAMTOOLS_SORMADUP", - "samtools", - "1.23.1" - ] - ], "bam": [ [ { "id": "test" }, - "test.bam:md5,706f3bc699aa89ae43868fcfd38a0d71" + "test.bam:md5,5ba398077fcb6258f65477176d82681e" ] ], "crai": [ @@ -166,15 +102,15 @@ [ "SAMTOOLS_SORMADUP", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T16:09:12.316289173", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:03:46.127216" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 946bb362..6a19f168 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.24 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.24 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 271f1a91..43f1de5f 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.24--d697cfb9dce007cd'}" input: tuple val(meta), path(bam), path(fasta), path(fai) diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index b60edf8c..035e91b6 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -15,11 +15,11 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) @@ -30,13 +30,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( - process.out.bam, - process.out.index, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -48,11 +48,11 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) @@ -63,13 +63,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( - process.out.bam, - process.out.index, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -81,11 +81,11 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) @@ -96,13 +96,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( - process.out.bam, - process.out.index, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -114,14 +114,14 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ] ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -132,13 +132,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( - process.out.bam, - process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -150,14 +150,14 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ] ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -168,13 +168,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( - process.out.bam, - process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -186,14 +186,14 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ] ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -204,13 +204,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( - process.out.bam, - process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -222,11 +222,11 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -237,13 +237,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + ).match() } ) } } @@ -256,11 +256,11 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) @@ -271,8 +271,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -285,14 +285,14 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ] ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -303,8 +303,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -318,11 +318,11 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -333,47 +333,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } } - test("multi_sam") { - - config "./nextflow_sam.config" - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.sam', checkIfExists: true) - ]) - input[1] = Channel.of([ - [ id:'fasta' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ]) - input[2] = '' - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot( - process.out.bam.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} - ) - } - } - - test("sam") { config "./nextflow_sam.config" @@ -381,12 +347,11 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.sam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.sam', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -397,13 +362,13 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.bam.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.findAll { key, val -> key.startsWith("versions") } - ).match()} + ).match() } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 5ce05c3c..43677f3c 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -24,27 +24,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T07:15:51.469358", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:36.491063" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "bam_csi_index": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,53aea06779611856bc481c60beabecaa" - ] + "test.sorted.bam:readsMD5,894549ee3ced6b5ca2eed2563a985217" ], [ [ @@ -52,7 +46,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam.csi:md5,f77a4adb3dde616d7eafd28db2ed147c" + "test.sorted.bam.csi:md5,43f545200e545ca2075c475d194a5130" ] ], { @@ -60,16 +54,16 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T17:05:03.136300204", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:14.341977" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "bam - stub": { "content": [ @@ -78,27 +72,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T09:04:43.558376", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:43.558376" + } }, "multiple bam bai index": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,a15f775c655d4a3b080812a8aae84d34" - ] + "test.sorted.bam:readsMD5,c4525b95f05075208347295e6a1fb232" ], [ [ @@ -114,16 +102,16 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T17:05:14.840145298", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:25.647565" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "cram - stub": { "content": [ @@ -132,27 +120,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T09:04:54.684578", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:54.684578" + } }, "multiple bam": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,f4343475d9ed2c261f31e1e49d67c1b6" - ] + "test.sorted.bam:readsMD5,c4525b95f05075208347295e6a1fb232" ], [ @@ -162,16 +144,16 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T17:05:09.324351486", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:20.2368" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "multiple bam - stub": { "content": [ @@ -180,51 +162,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-03-19T09:04:48.874947", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:48.874947" + } }, "bam_no_index": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,9277ba4bea590ae1b84e6ab06d11d79b" - ] - ], - [ - - ], - { - "versions_samtools": [ - [ - "SAMTOOLS_SORT", - "samtools", - "1.23.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:03.721646" - }, - "multi_sam": { - "content": [ - [ - + "test.sorted.bam:readsMD5,894549ee3ced6b5ca2eed2563a985217" ], [ @@ -234,27 +186,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T17:04:53.194840222", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:00.624092" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "multiple bam csi index": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,f168809dc154156c40548c06d0f46791" - ] + "test.sorted.bam:readsMD5,c4525b95f05075208347295e6a1fb232" ], [ [ @@ -270,16 +216,16 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T17:05:22.574450685", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:31.11865" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "sam": { "content": [ @@ -294,27 +240,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T07:19:30.478625", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:06.309319" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "bam_bai_index": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,2ca2d7f2368251d3f06f84afa49865a5" - ] + "test.sorted.bam:readsMD5,894549ee3ced6b5ca2eed2563a985217" ], [ [ @@ -322,7 +262,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,66dca3dc2e314029035799f6f44f60d1" + "test.sorted.bam.bai:md5,4810374728f259a493e1e61c90847da3" ] ], { @@ -330,15 +270,15 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T17:04:58.163543444", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:09.147615" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 946bb362..6a19f168 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -5,6 +5,6 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.24 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.24 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 144aa5e1..d7615fd2 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.24--d697cfb9dce007cd'}" input: tuple val(meta), path(input), path(input_index), path(fasta), path(fai) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index 140adf34..5059e296 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -25,9 +25,9 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -37,12 +37,12 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) @@ -52,9 +52,9 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -66,7 +66,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -77,9 +77,9 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -91,12 +91,12 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) ]) - input[1] = Channel.of([ + input[1] = channel.of([ [ id:'genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) @@ -106,9 +106,9 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 975d44a1..12eb0e47 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -2,65 +2,33 @@ "cram": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,e4d6cf0e75cebd0bafa84141e0b6929b" - ] - ], - "1": [ - [ - "SAMTOOLS_STATS", - "samtools", - "1.23.1" - ] - ], "stats": [ [ { "id": "test", "single_end": false }, - "test.stats:md5,e4d6cf0e75cebd0bafa84141e0b6929b" + "test.stats:md5,f8d811a048831b83812d55073566e67f" ] ], "versions_samtools": [ [ "SAMTOOLS_STATS", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T16:10:52.814596882", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:39.987454" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "bam - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "SAMTOOLS_STATS", - "samtools", - "1.23.1" - ] - ], "stats": [ [ { @@ -74,36 +42,20 @@ [ "SAMTOOLS_STATS", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T16:10:57.131242371", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:47.495502" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "cram - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "SAMTOOLS_STATS", - "samtools", - "1.23.1" - ] - ], "stats": [ [ { @@ -117,58 +69,42 @@ [ "SAMTOOLS_STATS", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T16:11:08.400007304", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:56.38373" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "bam": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,80f94eb0b68e213bdc8231109d3b43ad" - ] - ], - "1": [ - [ - "SAMTOOLS_STATS", - "samtools", - "1.23.1" - ] - ], "stats": [ [ { "id": "test", "single_end": false }, - "test.stats:md5,80f94eb0b68e213bdc8231109d3b43ad" + "test.stats:md5,2313c93da60ff8673a793b14a0886987" ] ], "versions_samtools": [ [ "SAMTOOLS_STATS", "samtools", - "1.23.1" + "1.24" ] ] } ], + "timestamp": "2026-07-10T16:10:38.846072426", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:24.59441" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index 76eee0d9..45638e8f 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -1,11 +1,11 @@ process SNAPALIGNER_ALIGN { - tag "$meta.id" + tag "${meta.id}" label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.5--h077b44d_2': - 'quay.io/biocontainers/snap-aligner:2.0.5--h077b44d_2' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.5--h077b44d_2' + : 'quay.io/biocontainers/snap-aligner:2.0.5--h077b44d_2'}" input: tuple val(meta) , path(reads, stageAs: "?/*"), path(index) @@ -32,12 +32,13 @@ process SNAPALIGNER_ALIGN { ${reads} \\ -o ${prefix}.bam \\ -t ${task.cpus} \\ - $args + ${args} """ stub: + def prefix = task.ext.prefix ?: "${meta.id}" """ - touch test.bam - touch test.bam.bai + touch ${prefix}.bam + touch ${prefix}.bam.bai """ } diff --git a/modules/nf-core/snapaligner/align/tests/main.nf.test b/modules/nf-core/snapaligner/align/tests/main.nf.test index 254ea40d..11f5c14f 100644 --- a/modules/nf-core/snapaligner/align/tests/main.nf.test +++ b/modules/nf-core/snapaligner/align/tests/main.nf.test @@ -45,9 +45,9 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, readsMD5Keys: ["bam"], unstableKeys: ["bai"])).match()} ) } } @@ -85,9 +85,9 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, readsMD5Keys: ["bam"], unstableKeys: ["bai"])).match()} ) } } @@ -130,9 +130,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/snapaligner/align/tests/main.nf.test.snap b/modules/nf-core/snapaligner/align/tests/main.nf.test.snap index f6107c9c..cc23c73f 100644 --- a/modules/nf-core/snapaligner/align/tests/main.nf.test.snap +++ b/modules/nf-core/snapaligner/align/tests/main.nf.test.snap @@ -2,38 +2,13 @@ "test_snapaligner_single": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,fc98a93036a3c5f7c674d470f7c5515a" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam.bai:md5,c46eb41ccbca7a9a9a8522e44c2cd490" - ] - ], - "2": [ - [ - "SNAPALIGNER_ALIGN", - "snap-aligner", - "2.0.5" - ] - ], "bai": [ [ { "id": "test", "single_end": true }, - "test.bam.bai:md5,c46eb41ccbca7a9a9a8522e44c2cd490" + "test.bam.bai" ] ], "bam": [ @@ -42,7 +17,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,fc98a93036a3c5f7c674d470f7c5515a" + "test.bam:md5Reads,f571f4ff5b2007b74cc9a509dd990910" ] ], "versions_snapaligner": [ @@ -54,40 +29,15 @@ ] } ], - "timestamp": "2026-02-18T13:58:48.808573", + "timestamp": "2026-08-31T14:12:28.627822436", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.08.0" } }, "test_snapaligner_stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "SNAPALIGNER_ALIGN", - "snap-aligner", - "2.0.5" - ] - ], "bai": [ [ { @@ -115,47 +65,22 @@ ] } ], - "timestamp": "2026-02-18T13:59:04.153824", + "timestamp": "2026-08-31T14:05:25.247591162", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.08.0" } }, "test_snapaligner_paired": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d4e6df5e063034da268fa4b97db369d3" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,d5979aec0109084091150ceb4d87d351" - ] - ], - "2": [ - [ - "SNAPALIGNER_ALIGN", - "snap-aligner", - "2.0.5" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.bam.bai:md5,d5979aec0109084091150ceb4d87d351" + "test.bam.bai" ] ], "bam": [ @@ -164,7 +89,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,d4e6df5e063034da268fa4b97db369d3" + "test.bam:md5Reads,831a859b2e75c55b6684baa858220a0c" ] ], "versions_snapaligner": [ @@ -176,10 +101,10 @@ ] } ], - "timestamp": "2026-02-18T13:58:57.101052", + "timestamp": "2026-08-31T14:12:36.668003605", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.08.0" } } } \ No newline at end of file diff --git a/modules/nf-core/strobealign/.conda-lock/linux_amd64-bd-90eb6a088ad3d321_1.txt b/modules/nf-core/strobealign/.conda-lock/linux_amd64-bd-90eb6a088ad3d321_1.txt new file mode 100644 index 00000000..66f2b336 --- /dev/null +++ b/modules/nf-core/strobealign/.conda-lock/linux_amd64-bd-90eb6a088ad3d321_1.txt @@ -0,0 +1,384 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/conda-forge/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: 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+size: 100332 +timestamp: 1785276566528 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h9d15635_7.conda +sha256: 427fd14bcb3b8659796fecc682716617409350fb5a98e5b7b47558a10d1a2fc7 +md5: d942e34ac3920ba83f8b2d0169570187 +depends: +- libzlib >=1.3.2,<2.0a0 +license: BSD-3-Clause +license_family: BSD +size: 615477 +timestamp: 1786599613561 diff --git a/modules/nf-core/strobealign/environment.yml b/modules/nf-core/strobealign/environment.yml index fc1f89b8..5e0bb840 100644 --- a/modules/nf-core/strobealign/environment.yml +++ b/modules/nf-core/strobealign/environment.yml @@ -3,7 +3,7 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.22.1 - - bioconda::samtools=1.22.1 - - bioconda::strobealign=0.16.1 + - bioconda::htslib=1.24 + - bioconda::samtools=1.24 + - bioconda::strobealign=0.17.0 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/strobealign/main.nf b/modules/nf-core/strobealign/main.nf index 4a416556..5118c086 100644 --- a/modules/nf-core/strobealign/main.nf +++ b/modules/nf-core/strobealign/main.nf @@ -3,22 +3,22 @@ process STROBEALIGN { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/59/59cce6872df48a1e5cc9ccee89f066210694c6ec9f62d9c931cc6925ca0f6a5f/data' : - 'community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:4fa4f439c6bea386' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/58/58b8968bb248307d133950891a33c9e569f5f1aa729ad997d8bb1311ec7f2589/data' + : 'community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:90eb6a088ad3d321'}" input: tuple val(meta) , path(reads), path(fasta), path(index) val sort_bam output: - tuple val(meta), path("*.bam") , emit: bam , optional: true - tuple val(meta), path("*.cram") , emit: cram, optional: true - tuple val(meta), path("*.csi") , emit: csi , optional: true - tuple val(meta), path("*.crai") , emit: crai, optional: true - tuple val(meta), path("*.paf.gz") , emit: paf , optional: true - tuple val(meta), path("*.tsv.gz") , emit: tsv , optional: true - tuple val(meta), path("*.sti") , emit: sti , optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.paf.gz"), emit: paf, optional: true + tuple val(meta), path("*.tsv.gz"), emit: tsv, optional: true + tuple val(meta), path("*.sti"), emit: sti, optional: true tuple val("${task.process}"), val('strobealign'), eval("strobealign --version"), topic: versions, emit: versions_strobealign tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions tuple val("${task.process}"), val('pigz'), eval("pigz --version 2>&1 | sed 's/pigz //'"), emit: versions_pigz, topic: versions @@ -89,8 +89,8 @@ process STROBEALIGN { touch ${prefix}.${extension} touch ${prefix}.csi touch ${prefix}.crai - echo "" | pigz > ${prefix}.paf.gz - echo "" | pigz > ${prefix}.tsv.gz + echo "" | gzip > ${prefix}.paf.gz + echo "" | gzip > ${prefix}.tsv.gz touch ${prefix}.sti """ } diff --git a/modules/nf-core/strobealign/meta.yml b/modules/nf-core/strobealign/meta.yml index f4b85b24..8ebe5be8 100644 --- a/modules/nf-core/strobealign/meta.yml +++ b/modules/nf-core/strobealign/meta.yml @@ -190,3 +190,27 @@ authors: maintainers: - "@matthdsm" - "@nvnieuwk" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:be473d108d6e0fb8 + build_id: bd-be473d108d6e0fb8_1 + scan_id: sc-1c7aa91ff75be091_1 + linux/amd64: + name: community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:90eb6a088ad3d321 + build_id: bd-90eb6a088ad3d321_1 + scan_id: sc-2d791fc8861014bc_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:38afc784dff2496a + build_id: bd-38afc784dff2496a_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/58/58b8968bb248307d133950891a33c9e569f5f1aa729ad997d8bb1311ec7f2589/data + linux/arm64: + name: oras://community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:90ad219a62d4fc12 + build_id: bd-90ad219a62d4fc12_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/54a576c51485cf7af3223084b2bfffabbe1c25c92c987ba564bb061ad0a16c89/data + conda: + linux/amd64: + lock_file: modules/nf-core/strobealign/.conda-lock/linux_amd64-bd-90eb6a088ad3d321_1.txt + linux/arm64: + lock_file: modules/nf-core/strobealign/.conda-lock/linux_arm64-bd-be473d108d6e0fb8_1.txt diff --git a/modules/nf-core/strobealign/tests/main.nf.test b/modules/nf-core/strobealign/tests/main.nf.test index adab50bc..9786e8e0 100644 --- a/modules/nf-core/strobealign/tests/main.nf.test +++ b/modules/nf-core/strobealign/tests/main.nf.test @@ -1,5 +1,3 @@ -// TODO nf-core: Once you have added the required tests, please run the following command to build this file: -// nf-core modules test strobealign nextflow_process { name "Test Process STROBEALIGN" @@ -39,11 +37,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.bam, - process.out.csi, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } + { assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"])).match() } ) } } @@ -76,10 +70,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.bam, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } + { assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"])).match() } ) } } @@ -112,11 +103,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - cram(process.out.cram[0][1], 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta').getReadsMD5(), - file(process.out.crai[0][1]).exists(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } + { assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["cram"], unstableKeys:["crai"], referenceFasta: 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta')).match() } // for cram files ) } } @@ -149,10 +136,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - cram(process.out.cram[0][1], 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta').getReadsMD5(), - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } + { assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["cram"], unstableKeys:["crai"], referenceFasta: 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta')).match() } // for cram files ) } } @@ -185,10 +169,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.paf, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -221,10 +202,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.tsv, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -257,10 +235,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.sti, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -294,10 +269,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/strobealign/tests/main.nf.test.snap b/modules/nf-core/strobealign/tests/main.nf.test.snap index 7e53f32d..d7b33922 100644 --- a/modules/nf-core/strobealign/tests/main.nf.test.snap +++ b/modules/nf-core/strobealign/tests/main.nf.test.snap @@ -1,50 +1,40 @@ { "fastq - sorted cram": { "content": [ - "f3a1593b170cf1e9b9008b3afb77cc53", - true, { - "versions_pigz": [ - [ - "STROBEALIGN", - "pigz", - "2.8" - ] + "bam": [ + ], - "versions_samtools": [ + "crai": [ [ - "STROBEALIGN", - "samtools", - "1.22.1" + { + "id": "test", + "single_end": false + }, + "test.cram.crai" ] ], - "versions_strobealign": [ + "cram": [ [ - "STROBEALIGN", - "strobealign", - "0.16.1" + { + "id": "test", + "single_end": false + }, + "test.cram:md5Reads,f3a1593b170cf1e9b9008b3afb77cc53" ] - ] - } - ], - "timestamp": "2026-02-18T14:11:52.319915", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "fastq - sti": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.r150.sti:md5,1fa95f6ba0167a729ddc6a444eb5e8f7" - ] - ], - { + ], + "csi": [ + + ], + "paf": [ + + ], + "sti": [ + + ], + "tsv": [ + + ], "versions_pigz": [ [ "STROBEALIGN", @@ -56,28 +46,54 @@ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], "versions_strobealign": [ [ "STROBEALIGN", "strobealign", - "0.16.1" + "0.17.0" ] ] } ], - "timestamp": "2026-02-18T14:12:18.718682", + "timestamp": "2026-08-25T14:25:34.701002", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, - "fastq - unsorted cram": { + "fastq - sti": { "content": [ - "57aeef88ed701a8ebc8e2f0a381b2a6", { + "bam": [ + + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "paf": [ + + ], + "sti": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.r150.sti:md5,01b9b2d75dac3b57a66333eced63a5bc" + ] + ], + "tsv": [ + + ], "versions_pigz": [ [ "STROBEALIGN", @@ -89,36 +105,54 @@ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], "versions_strobealign": [ [ "STROBEALIGN", "strobealign", - "0.16.1" + "0.17.0" ] ] } ], - "timestamp": "2026-02-18T14:11:59.009249", + "timestamp": "2026-08-25T15:07:54.583376", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, - "fastq - tsv": { + "fastq - unsorted cram": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv.gz:md5,1fcb7444ba029b7f41b3a836fec7ecac" - ] - ], { + "bam": [ + + ], + "crai": [ + + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5Reads,57aeef88ed701a8ebc8e2f0a381b2a6" + ] + ], + "csi": [ + + ], + "paf": [ + + ], + "sti": [ + + ], + "tsv": [ + + ], "versions_pigz": [ [ "STROBEALIGN", @@ -130,105 +164,86 @@ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], "versions_strobealign": [ [ "STROBEALIGN", "strobealign", - "0.16.1" + "0.17.0" ] ] } ], - "timestamp": "2026-02-18T14:12:12.224719", + "timestamp": "2026-08-25T14:25:40.564007", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, - "stub": { + "fastq - tsv": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "bam": [ + ], - "1": [ + "crai": [ ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "cram": [ + ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "csi": [ + ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "paf": [ + ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "sti": [ + ], - "6": [ + "tsv": [ [ { "id": "test", "single_end": false }, - "test.sti:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.tsv.gz:md5,1fcb7444ba029b7f41b3a836fec7ecac" ] ], - "7": [ + "versions_pigz": [ [ "STROBEALIGN", - "strobealign", - "0.16.1" + "pigz", + "2.8" ] ], - "8": [ + "versions_samtools": [ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], - "9": [ + "versions_strobealign": [ [ "STROBEALIGN", - "pigz", - "2.8" + "strobealign", + "0.17.0" ] - ], + ] + } + ], + "timestamp": "2026-08-25T15:07:49.62725", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "stub": { + "content": [ + { "bam": [ [ { @@ -297,36 +312,54 @@ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], "versions_strobealign": [ [ "STROBEALIGN", "strobealign", - "0.16.1" + "0.17.0" ] ] } ], - "timestamp": "2026-02-18T14:12:25.287429", + "timestamp": "2026-08-25T15:07:59.707297", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "fastq - unsorted bam": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,740d88010349b3cd487a8b6244c64c0d" - ] - ], { + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5Reads,57aeef88ed701a8ebc8e2f0a381b2a6" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "paf": [ + + ], + "sti": [ + + ], + "tsv": [ + + ], "versions_pigz": [ [ "STROBEALIGN", @@ -338,36 +371,54 @@ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], "versions_strobealign": [ [ "STROBEALIGN", "strobealign", - "0.16.1" + "0.17.0" ] ] } ], - "timestamp": "2026-02-18T14:11:44.848089", + "timestamp": "2026-08-25T15:07:23.733668", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "fastq - paf": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.paf.gz:md5,0992a1eb3dff9beca5849b9d1fc66390" - ] - ], { + "bam": [ + + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "paf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paf.gz:md5,b154778d9264943e0a8888d9251c7b6e" + ] + ], + "sti": [ + + ], + "tsv": [ + + ], "versions_pigz": [ [ "STROBEALIGN", @@ -379,45 +430,60 @@ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], "versions_strobealign": [ [ "STROBEALIGN", "strobealign", - "0.16.1" + "0.17.0" ] ] } ], - "timestamp": "2026-02-18T14:12:05.638183", + "timestamp": "2026-08-25T15:07:44.105176", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "fastq - sorted bam": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,c9bf092d8998eac47b6b85afe9aa9038" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.csi:md5,8d53854f92b3f263db0ed27f4bbad054" - ] - ], { + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5Reads,f3a1593b170cf1e9b9008b3afb77cc53" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.csi:md5,4824d78e96e78a803b60853e747c3dc0" + ] + ], + "paf": [ + + ], + "sti": [ + + ], + "tsv": [ + + ], "versions_pigz": [ [ "STROBEALIGN", @@ -429,22 +495,22 @@ [ "STROBEALIGN", "samtools", - "1.22.1" + "1.24" ] ], "versions_strobealign": [ [ "STROBEALIGN", "strobealign", - "0.16.1" + "0.17.0" ] ] } ], - "timestamp": "2026-02-18T14:11:38.040997", + "timestamp": "2026-08-25T15:07:17.578477", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 20e156f9..9fa264dc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -8,24 +8,59 @@ // Global default params, used in configs params { - igenomes_base = '/references/' - igenomes_ignore = false + // Input options + input = null + + // Pipeline options + split_fastq = 0 + genelists = null + + // References + igenomes_base = '/references' + genomes = [:] + + // MultiQC options + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' + + // Boilerplate options + outdir = './results' publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false monochrome_logs = false - hook_url = System.getenv('HOOK_URL') + help = false + help_full = false + show_hidden = false + version = false + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') - custom_config_version = 'main' - custom_config_base = "https://raw.githubusercontent.com/nf-cmgg/configs/${params.custom_config_version}" + // Config options + config_profile_name = null + config_profile_description = null + + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_url = null + + // Schema validation default options + validate_params = true } +// Backwards compatibility for publishDir syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + // Load base.config by default for all pipelines includeConfig 'conf/base.config' - -// Load igenomes.config if required -includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' +includeConfig 'conf/igenomes.config' profiles { debug { @@ -52,10 +87,21 @@ profiles { singularity.ociAutoPull = true wave.enabled = true wave.freeze = true - wave.strategy = ["conda", "container"] + wave.strategy = 'conda,container' + } + apple { + appleContainer.enabled = true + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + singularity.enabled = false } emulate_amd64 { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + appleContainer.runOptions = '-u $(id -u):$(id -g) --arch amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true @@ -109,7 +155,7 @@ profiles { singularity.ociAutoPull = true wave.enabled = true wave.freeze = true - wave.strategy = ["conda", "container"] + wave.strategy = 'conda,container' } gpu { docker.runOptions = '-u $(id -u):$(id -g) --gpus all' @@ -134,6 +180,7 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa // Load nf-cmgg/preprocessing custom profiles from different institutions. includeConfig params.custom_config_base && params.custom_config_base.contains('nf-cmgg') && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/preprocessing.config" : "/dev/null" + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -146,7 +193,7 @@ env { } // Set bash options -process.shell = ["bash", "-C", "-e", "-u", "-o", "pipefail"].join(' ') +process.shell = ["bash", "-C", "-e", "-u", "-o", "pipefail"] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -169,7 +216,7 @@ trace { dag { enabled = true overwrite = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.mmd" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { @@ -195,26 +242,21 @@ manifest { homePage = 'https://github.com/nf-cmgg/preprocessing' description = """Demultiplexing, adapter trimming, alignment, and coverage calculation for NGS data.""" mainScript = 'main.nf' - defaultBranch = 'main' + defaultBranch = 'master' nextflowVersion = '!>=26.04.0' - version = '3.0.2' + version = '3.1.0' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.7.2' + id 'nf-schema@3.0.0' + id 'nf-teams@0.2.0' } validation { - defaultIgnoreParams = ["genomes"].toSet() - monochromeLogs = params.monochrome_logs.toBoolean() + defaultIgnoreParams = ["genomes"] + monochromeLogs = params.monochrome_logs } - // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' - -// Set default output dir and publish mode -// Temporary fix until the nf-core template supports workflow output definitions -workflow.output.mode = params.publish_dir_mode -outputDir = params.outdir diff --git a/nextflow_schema.json b/nextflow_schema.json index 36936165..e0f31be3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,10 +15,11 @@ "input": { "type": "string", "format": "file-path", + "mimetype": "text/csv", "exists": true, "schema": "assets/schema_input.json", "pattern": "^\\S+\\.(csv|tsv|yaml|yml|json)$", - "description": "Path to comma-separated or yaml file containing information about the samples in the experiment.", + "description": "Path to a file containing information about the samples in the experiment. Supported formats are CSV, TSV, YAML, and JSON.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location.", "fa_icon": "fas fa-file-csv" }, @@ -39,10 +40,6 @@ "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" - }, - "genomes": { - "type": "object", - "hidden": true } } }, @@ -62,7 +59,7 @@ "const": 0 } ], - "default": 100000000, + "default": 0, "fa_icon": "fas fa-clock", "description": "Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.", "help_text": "Use the the tool FastP to split FASTQ file by number of reads. This parallelizes across fastq file shards speeding up mapping. Note although the minimum value is 250 reads, if you have fewer than 250 reads a single FASTQ shard will still be created." @@ -76,6 +73,26 @@ } } }, + "reference_genome_options": { + "title": "Reference genome options", + "type": "object", + "fa_icon": "fas fa-dna", + "description": "Reference genome related files and options required for the workflow.", + "properties": { + "genomes": { + "type": "object", + "description": "Map of genome keys to reference files. Populated from `conf/igenomes.config`.", + "hidden": true + }, + "igenomes_base": { + "type": "string", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "/references" + } + } + }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -86,16 +103,16 @@ "custom_config_version": { "type": "string", "description": "Git commit id for Institutional configs.", - "default": "main", + "default": "master", "hidden": true, "fa_icon": "fas fa-users-cog" }, "custom_config_base": { "type": "string", - "description": "Base directory for custom configs.", - "default": "https://raw.githubusercontent.com/nf-cmgg/configs/main", + "description": "Base directory for Institutional configs.", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", "hidden": true, - "help_text": "If you're running offline, Nextflow will not be able to fetch the custom config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", + "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", "fa_icon": "fas fa-users-cog" }, "config_profile_name": { @@ -174,13 +191,6 @@ "fa_icon": "fas fa-palette", "hidden": true }, - "hook_url": { - "type": "string", - "description": "Incoming hook URL for messaging service", - "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", - "hidden": true - }, "multiqc_config": { "type": "string", "format": "file-path", @@ -194,11 +204,6 @@ "fa_icon": "fas fa-image", "hidden": true }, - "multiqc_methods_description": { - "type": "string", - "description": "Custom MultiQC yaml file containing HTML including a methods description.", - "fa_icon": "fas fa-cog" - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -206,6 +211,13 @@ "fa_icon": "fas fa-check-square", "hidden": true }, + "modules_testdata_base_path": { + "type": "string", + "fa_icon": "far fa-check-circle", + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", + "hidden": true + }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -230,27 +242,6 @@ "show_hidden": { "type": "boolean", "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)." - }, - "igenomes_base": { - "type": "string", - "format": "directory-path", - "description": "Directory / URL base for iGenomes references.", - "fa_icon": "fas fa-cloud-download-alt", - "default": "/references/", - "hidden": true - }, - "igenomes_ignore": { - "type": "boolean", - "description": "Do not load the iGenomes reference config.", - "fa_icon": "fas fa-ban", - "hidden": true, - "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." - }, - "genome": { - "type": "string", - "description": "Name of iGenomes reference.", - "fa_icon": "fas fa-book", - "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." } } } @@ -262,6 +253,9 @@ { "$ref": "#/$defs/pipeline_options" }, + { + "$ref": "#/$defs/reference_genome_options" + }, { "$ref": "#/$defs/institutional_config_options" }, diff --git a/nf-test.config b/nf-test.config index bda04274..4ac516e9 100644 --- a/nf-test.config +++ b/nf-test.config @@ -9,16 +9,32 @@ config { configFile = "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'] + ignore = [ + 'modules/nf-core/**/tests/*', + 'subworkflows/nf-core/**/tests/*', + ] // run all test with defined profile(s) from the main nextflow.config - profile = "test,s3_ugent" + profile = "test" // list of filenames or patterns that should be trigger a full test run - triggers = ['nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'] + triggers = [ + '.github/actions/nf-test/action.yml', + '.github/workflows/nf-test.yml', + 'assets/schema_input.json', + 'bin/*', + 'conf/test.config', + 'nextflow.config', + 'nextflow_schema.json', + 'nf-test.config', + 'tests/.nftignore', + 'tests/nextflow.config', + ] // load the necessary plugins plugins { - load "nft-utils@0.0.7" + load "nft-bam@0.7.0" + load "nft-vcf@1.0.7" + load "nft-utils@1.1.1" } } diff --git a/pixi.lock b/pixi.lock index d7613388..537fe094 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,8 +1,16 @@ version: 7 platforms: - name: linux-64 - - name: osx-64 + virtual-packages: + - __unix=0=0 + - __linux=4.18 + - __glibc=2.28 + - __archspec=0=x86_64 - name: osx-arm64 + virtual-packages: + - __unix=0=0 + - __osx=13.0 + - __archspec=0=m1 environments: default: channels: @@ -10,8 +18,9 @@ environments: - url: https://conda.anaconda.org/bioconda/ packages: linux-64: - - conda: https://conda.anaconda.org/bioconda/noarch/nextflow-26.04.1-h2a3209d_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/nf-core-4.0.2-pyhdfd78af_1.conda + - conda: https://conda.anaconda.org/bioconda/noarch/nextflow-26.04.6-h2a3209d_1.conda + - conda: https://conda.anaconda.org/bioconda/noarch/nf-core-4.1.0-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/nf-metro-2.0.0-pyhdfd78af_0.conda - 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[dependencies] -nextflow = ">=26.4.1,<27" +nextflow = ">=26.4.6,<27" nf-test = ">=0.9.5,<0.10" prek = ">=0.3.13,<0.4" -nf-core = ">=4.0.2,<5" +nf-core = ">=4.1.0,<5" +nf-metro = ">=2.0.0,<3" diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 56110621..00000000 --- a/pyproject.toml +++ /dev/null @@ -1,15 +0,0 @@ -# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff. -# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.ruff] -line-length = 120 -target-version = "py38" -cache-dir = "~/.cache/ruff" - -[tool.ruff.lint] -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] - -[tool.ruff.lint.isort] -known-first-party = ["nf_core"] - -[tool.ruff.lint.per-file-ignores] -"__init__.py" = ["E402", "F401"] diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index e66cfe12..e9665e5a 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -1,6 +1,6 @@ { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", { "GithubService": "https://w3id.org/ro/terms/test#GithubService", "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2026-05-27T13:33:39+00:00", - "description": "# nf-cmgg/preprocessing\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-cmgg/preprocessing)\n[![GitHub Actions CI Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-cmgg/preprocessing)\n\n## Introduction\n\n**nf-cmgg/preprocessing** is a bioinformatics pipeline that demultiplexes and aligns raw sequencing data.\nIt also performs basic QC and coverage analysis.\n\nThe pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.\n\nSteps include:\n\n- Demultiplexing using [`BCLconvert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)\n- Run QC using [`MultiQC SAV`](https://github.com/MultiQC/MultiQC_SAV)\n- Read QC and trimming using [`fastp`](https://github.com/OpenGene/fastp) or [`falco`](https://github.com/smithlabcode/falco)\n- Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq\n- Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html)\n- Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html)\n- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollectHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics)\n- QC aggregation using [`multiqc`](https://multiqc.info/)\n\n\n\n \n \n \"Fallback\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nThe full documentation can be found [here](docs/README.md)\n\nFirst, prepare a samplesheet with your input data. Check the [usage docs](docs/usage.md) for details on the required format and example files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-cmgg/preprocessing \\\n -profile \\\n --igenomes_base /path/to/genomes \\\n --input samplesheet. \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\n## Development environment\n\nA [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:\n\n```\npixi install\n```\n\nThen run `pixi shell` to enter the environment and start developing.\n\n## Credits\n\nnf-cmgg/preprocessing was originally written by the CMGG ICT team.\n\n## Support\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-09-17T12:15:21+00:00", + "description": "# nf-cmgg/preprocessing\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-cmgg/preprocessing)\n[![GitHub Actions CI Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n\n## Introduction\n\n**nf-cmgg/preprocessing** is a bioinformatics pipeline that demultiplexes and aligns raw sequencing data.\nIt also performs basic QC and coverage analysis.\n\nThe pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.\n\nSteps include:\n\n- Demultiplexing using [`BCL Convert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)\n- Run QC using [`MultiQC SAV`](https://github.com/MultiQC/MultiQC_SAV)\n- Read QC and adapter trimming using [`fastp`](https://github.com/OpenGene/fastp). Samples without a supported genome or with `aligner` set to `false` skip alignment and are QC'd with [`falco`](https://github.com/smithlabcode/falco) instead\n- Alignment using [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobealign`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq\n- UMI consensus (`call_consensus`) using [`fgumi`](https://github.com/fulcrumgenomics/fgbio) with SNAP\n- Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html)\n- Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and, in `qc_mode: full`, [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html)\n- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and, in `qc_mode: full`, [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html) and [`riker multi`](https://github.com/fulcrumgenomics/riker)\n- QC aggregation using [`MultiQC`](https://multiqc.info/)\n\n\n\n \n \n \"nf-cmgg/preprocessing\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nThe full documentation can be found [here](docs/README.md)\n\nFirst, prepare a samplesheet with your input data. Check the [usage docs](docs/usage.md) for details on the required format and example files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-cmgg/preprocessing \\\n -profile \\\n --igenomes_base /path/to/genomes \\\n --input samplesheet. \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\n## Development environment\n\nA [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:\n\n```\npixi install\n```\n\nThen run `pixi shell` to enter the environment and start developing.\n\n## Credits\n\nnf-cmgg/preprocessing was originally written by the CMGG ICT team.\n\nAn extensive list of references for the tools used by the pipeline can be found in [`CITATIONS.md`](CITATIONS.md).\n\n## Support\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#cb12ae76-cc32-4dd8-b67d-d06d643513d2" + "@id": "#9d686fd1-ff35-4b80-b3c4-3a715cab35ee" } ], "name": "nf-cmgg/preprocessing" @@ -115,7 +115,7 @@ }, "conformsTo": [ { - "@id": "https://w3id.org/ro/crate/1.1" + "@id": "https://w3id.org/ro/crate/1.2" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -134,11 +134,8 @@ "@id": "https://orcid.org/0000-0003-2555-3114" } ], - "dateCreated": [ - "", - "2026-05-20T09:02:37Z" - ], - "dateModified": "2026-05-27T15:33:39Z", + "dateCreated": "", + "dateModified": "2026-09-17T14:15:21Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -166,10 +163,10 @@ }, "url": [ "https://github.com/nf-cmgg/preprocessing", - "https://nf-co.re/nf-cmgg/preprocessing/3.0.2/" + "https://nf-co.re/nf-cmgg/preprocessing/3.1.0/" ], "version": [ - "3.0.2" + "3.1.0" ] }, { @@ -185,11 +182,11 @@ "version": "!>=26.04.0" }, { - "@id": "#cb12ae76-cc32-4dd8-b67d-d06d643513d2", + "@id": "#9d686fd1-ff35-4b80-b3c4-3a715cab35ee", "@type": "TestSuite", "instance": [ { - "@id": "#f36a54e6-3b86-47eb-8f1d-f94369a34a5c" + "@id": "#269d11e9-19b2-4c15-a85a-9d6224139757" } ], "mainEntity": { @@ -198,7 +195,7 @@ "name": "Test suite for nf-cmgg/preprocessing" }, { - "@id": "#f36a54e6-3b86-47eb-8f1d-f94369a34a5c", + "@id": "#269d11e9-19b2-4c15-a85a-9d6224139757", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-cmgg/preprocessing", "resource": "repos/nf-cmgg/preprocessing/actions/workflows/nf-test.yml", diff --git a/subworkflows/local/bam_qc/main.nf b/subworkflows/local/bam_qc/main.nf index fb2452b2..8b6ac6e0 100644 --- a/subworkflows/local/bam_qc/main.nf +++ b/subworkflows/local/bam_qc/main.nf @@ -1,64 +1,134 @@ -// samtools modules -include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' - -// picard modules -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main' -include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main' -include { PICARD_COLLECTWGSMETRICS } from '../../../modules/nf-core/picard/collectwgsmetrics/main' +include { MOSDEPTH } from "../../../modules/nf-core/mosdepth/main.nf" +include { PANELCOVERAGE } from "../../../modules/local/panelcoverage/main" +include { RIKER_MULTI } from '../../../modules/nf-core/riker/multi/main' +include { SAMTOOLS_COVERAGE } from "../../../modules/nf-core/samtools/coverage/main" +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' workflow BAM_QC { take: - ch_bam_bai_roi_fasta_fai_dict // channel: [ val(meta), path(bam), path(bai), path(roi), path(fasta), path(fai), path(dict)] + ch_bam_bai_roi_fasta_fai_gtf // channel: [ val(meta), path(bam), path(bai), path(roi), path(fasta), path(fai), path(gtf)] + ch_genelists // channel: [optional] [genelists] main: - ch_bam_bai_roi_fasta_fai_dict - .map { meta, bam, bai, _roi, fasta, fai, _dict -> + + ch_bam_bai_roi_fasta_fai_gtf + .map { meta, bam, bai, _roi, fasta, fai, _gtf -> return [meta, bam, bai, fasta, fai] } .set { ch_bam_bai_fasta_fai } - SAMTOOLS_STATS(ch_bam_bai_fasta_fai) - SAMTOOLS_FLAGSTAT(ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> return [meta, bam, bai] }) - SAMTOOLS_IDXSTATS(ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> return [meta, bam, bai] }) + // basic QC + SAMTOOLS_FLAGSTAT( + ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> + return [meta, bam, bai] + } + ) + SAMTOOLS_IDXSTATS( + ch_bam_bai_fasta_fai.map { meta, bam, bai, _fasta, _fai -> + return [meta, bam, bai] + } + ) + + MOSDEPTH( + ch_bam_bai_roi_fasta_fai_gtf.map { meta, bam, bai, roi, fasta, _fai, _gtf -> + return [meta, bam, bai, roi, fasta] + }, + ['NO_COVERAGE', 'LOW_COVERAGE', 'CALLABLE'], + ) - ch_picard_hsmetrics = channel.empty() - ch_picard_multiplemetrics = channel.empty() - ch_picard_multiplemetrics_pdf = channel.empty() - ch_picard_wgsmetrics = channel.empty() + // full QC + // Only run on samples requiring full QC + ch_full_qc = ch_bam_bai_roi_fasta_fai_gtf.filter { meta, _bam, _bai, _roi, _fasta, _fai, _gtf -> + meta.qc_mode == "full" + } - ch_bam_bai_roi_fasta_fai_dict - .filter { meta, _bam, _bai, _roi, _fasta, _fai, _dict -> - !meta.disable_picard_metrics + SAMTOOLS_STATS( + ch_full_qc.map { meta, bam, bai, _roi, fasta, fai, _gtf -> + return [meta, bam, bai, fasta, fai] } - .set { ch_picard } + ) - PICARD_COLLECTMULTIPLEMETRICS(ch_picard) - ch_picard_multiplemetrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics - ch_picard_multiplemetrics_pdf = PICARD_COLLECTMULTIPLEMETRICS.out.pdf - ch_picard - .branch { meta, bam, bai, roi, fasta, fai, dict -> - hsmetrics: roi != [] - return [meta, bam, bai, roi, roi, fasta, fai, dict] - wgsmetrics: roi == [] - return [meta, bam, bai, fasta, fai, dict] + // RIKER_MULTI (meta, bam, bai, error_vcf, error_vcf_idx, error_intervals, gcbias_exclude_intervals, hybcap_baits, hybcap_targets, rna_gene_model, rna_ribosomal_intervals, wgs_intervals, fasta, fai) + RIKER_MULTI( + ch_full_qc.map { meta, bam, bai, roi, fasta, fai, gtf -> + return [ + meta, + bam, + bai, + [], + [], + [], + [], + roi, + roi, + gtf, + [], + [], + fasta, + fai, + ] } - .set { ch_picard_coverage } + ) - PICARD_COLLECTWGSMETRICS(ch_picard_coverage.wgsmetrics, []) - ch_picard_wgsmetrics = PICARD_COLLECTWGSMETRICS.out.metrics + SAMTOOLS_COVERAGE( + ch_full_qc.map { meta, bam, bai, _roi, fasta, fai, _gtf -> + return [meta, bam, bai, fasta, fai] + } + ) - PICARD_COLLECTHSMETRICS(ch_picard_coverage.hsmetrics) - ch_picard_hsmetrics = PICARD_COLLECTHSMETRICS.out.metrics + PANELCOVERAGE( + MOSDEPTH.out.per_base_bed.join(MOSDEPTH.out.per_base_csi).combine(ch_genelists).filter { meta, _bed, _index, _genelists -> meta.qc_mode == "full" }.map { meta, bed, index, genelists -> + // Because groovy typing sucks ass; apparently an array of 1 is automatically converted to a string... + if (genelists !instanceof List) { + genelists = [genelists] + } + def filtered_genelists = (meta.tag && meta.tag.toLowerCase() == "seqcap") + ? genelists.findAll { genelist -> genelist.name.toLowerCase().contains("seqcap") } + : genelists.findAll { genelist -> !genelist.name.toLowerCase().contains("seqcap") } + return [meta, bed, index, filtered_genelists] + }.filter { _meta, _bed, _index, filtered_genelists -> filtered_genelists.size() > 0 } + ) emit: - samtools_stats = SAMTOOLS_STATS.out.stats - samtools_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat - samtools_idxstats = SAMTOOLS_IDXSTATS.out.idxstats - picard_multiplemetrics = ch_picard_multiplemetrics - picard_multiplemetrics_pdf = ch_picard_multiplemetrics_pdf - picard_wgsmetrics = ch_picard_wgsmetrics - picard_hsmetrics = ch_picard_hsmetrics + mosdepth_global = MOSDEPTH.out.global_txt + mosdepth_per_base_bed = MOSDEPTH.out.per_base_bed + mosdepth_per_base_csi = MOSDEPTH.out.per_base_csi + mosdepth_per_base_d4 = MOSDEPTH.out.per_base_d4 + mosdepth_quantized_bed = MOSDEPTH.out.quantized_bed + mosdepth_quantized_csi = MOSDEPTH.out.quantized_csi + mosdepth_regions = MOSDEPTH.out.regions_txt + mosdepth_regions_bed = MOSDEPTH.out.regions_bed + mosdepth_regions_csi = MOSDEPTH.out.regions_csi + mosdepth_summary = MOSDEPTH.out.summary_txt + mosdepth_thresholds_bed = MOSDEPTH.out.thresholds_bed + mosdepth_thresholds_csi = MOSDEPTH.out.thresholds_csi + panelcoverage = PANELCOVERAGE.out.regiondist + riker_alignment_metrics = RIKER_MULTI.out.alignment_metrics + riker_base_dist = RIKER_MULTI.out.base_dist + riker_mean_qual = RIKER_MULTI.out.mean_qual + riker_qual_dist = RIKER_MULTI.out.qual_dist + riker_error_mismatch = RIKER_MULTI.out.error_mismatch + riker_error_overlap = RIKER_MULTI.out.error_overlap + riker_error_indel = RIKER_MULTI.out.error_indel + riker_gcbias_detail = RIKER_MULTI.out.gcbias_detail + riker_gcbias_summary = RIKER_MULTI.out.gcbias_summary + riker_hybcap_metrics = RIKER_MULTI.out.hybcap_metrics + riker_hybcap_per_target = RIKER_MULTI.out.hybcap_per_target + riker_hybcap_per_base = RIKER_MULTI.out.hybcap_per_base + riker_isize_metrics = RIKER_MULTI.out.isize_metrics + riker_isize_histogram = RIKER_MULTI.out.isize_histogram + riker_wgs_metrics = RIKER_MULTI.out.wgs_metrics + riker_wgs_coverage = RIKER_MULTI.out.wgs_coverage + riker_pdf = RIKER_MULTI.out.pdf + riker_rna_biotype = RIKER_MULTI.out.rna_biotype + riker_rna_insert_size_histogram = RIKER_MULTI.out.rna_insert_size_histogram + riker_rna_insert_size = RIKER_MULTI.out.rna_insert_size + riker_rna_metrics = RIKER_MULTI.out.rna_metrics + samtools_coverage = SAMTOOLS_COVERAGE.out.coverage + samtools_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat + samtools_idxstats = SAMTOOLS_IDXSTATS.out.idxstats + samtools_stats = SAMTOOLS_STATS.out.stats } diff --git a/subworkflows/local/bam_qc/meta.yml b/subworkflows/local/bam_qc/meta.yml index e69de29b..b576a8c4 100644 --- a/subworkflows/local/bam_qc/meta.yml +++ b/subworkflows/local/bam_qc/meta.yml @@ -0,0 +1,148 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "BAM_QC" +description: Alignment QC, coverage, riker metrics, and optional panel coverage +keywords: + - bam + - qc + - coverage + - mosdepth + - riker + - samtools +components: + - mosdepth + - panelcoverage + - riker/multi + - samtools/coverage + - samtools/flagstat + - samtools/idxstats + - samtools/stats +input: + - ch_bam_bai_roi_fasta_fai_gtf: + type: file + description: | + Aligned BAM, index, ROI, and references. + + Structure: [ val(meta), path(bam), path(bai), path(roi), path(fasta), path(fai), path(gtf) ] + - ch_genelists: + type: file + description: Optional gene-list BED files for panel coverage +output: + - mosdepth_global: + type: file + description: mosdepth global distribution + - mosdepth_per_base_bed: + type: file + description: mosdepth per-base BED + - mosdepth_per_base_csi: + type: file + description: Index for mosdepth per-base BED + - mosdepth_per_base_d4: + type: file + description: mosdepth per-base d4 + - mosdepth_quantized_bed: + type: file + description: mosdepth quantized BED + - mosdepth_quantized_csi: + type: file + description: Index for mosdepth quantized BED + - mosdepth_regions: + type: file + description: mosdepth regions summary + - mosdepth_regions_bed: + type: file + description: mosdepth regions BED + - mosdepth_regions_csi: + type: file + description: Index for mosdepth regions BED + - mosdepth_summary: + type: file + description: mosdepth summary + - mosdepth_thresholds_bed: + type: file + description: mosdepth thresholds BED + - mosdepth_thresholds_csi: + type: file + description: Index for mosdepth thresholds BED + - panelcoverage: + type: file + description: Panel coverage region distributions + - riker_alignment_metrics: + type: file + description: riker alignment metrics + - riker_base_dist: + type: file + description: riker base distribution + - riker_mean_qual: + type: file + description: riker mean quality + - riker_qual_dist: + type: file + description: riker quality distribution + - riker_error_mismatch: + type: file + description: riker mismatch error metrics + - riker_error_overlap: + type: file + description: riker overlap error metrics + - riker_error_indel: + type: file + description: riker indel error metrics + - riker_gcbias_detail: + type: file + description: riker GC bias detail + - riker_gcbias_summary: + type: file + description: riker GC bias summary + - riker_hybcap_metrics: + type: file + description: riker hybrid capture metrics + - riker_hybcap_per_target: + type: file + description: riker hybrid capture per-target metrics + - riker_hybcap_per_base: + type: file + description: riker hybrid capture per-base metrics + - riker_isize_metrics: + type: file + description: riker insert size metrics + - riker_isize_histogram: + type: file + description: riker insert size histogram + - riker_wgs_metrics: + type: file + description: riker WGS metrics + - riker_wgs_coverage: + type: file + description: riker WGS coverage + - riker_pdf: + type: file + description: riker PDF plots + - riker_rna_biotype: + type: file + description: riker RNA biotype metrics + - riker_rna_insert_size_histogram: + type: file + description: riker RNA insert size histogram + - riker_rna_insert_size: + type: file + description: riker RNA insert size metrics + - riker_rna_metrics: + type: file + description: riker RNA metrics + - samtools_coverage: + type: file + description: samtools coverage + - samtools_flagstat: + type: file + description: samtools flagstat + - samtools_idxstats: + type: file + description: samtools idxstats + - samtools_stats: + type: file + description: samtools stats +authors: + - "@matthdsm" +maintainers: + - "@matthdsm" + - "@nvnieuwk" diff --git a/subworkflows/local/bam_qc/tests/main.nf.test b/subworkflows/local/bam_qc/tests/main.nf.test new file mode 100644 index 00000000..d404fed7 --- /dev/null +++ b/subworkflows/local/bam_qc/tests/main.nf.test @@ -0,0 +1,156 @@ +nextflow_workflow { + + name "Test Workflow BAM_QC" + script "subworkflows/local/bam_qc/main.nf" + workflow "BAM_QC" + + tag "subworkflows" + tag "subworkflows/local" + tag "subworkflows/local/bam_qc" + + test("bam QC - basic - no roi") { + + when { + workflow { + """ + // [meta, bam, bai, roi, fasta, fai, gtf] + input[0] = Channel.of([ + [ id:'test', single_end:false, qc_mode:'basic' ], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), + [], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf", checkIfExists: true) + ]) + // genelists + def genelists_path = "s3://test-data/genomics/homo_sapiens/genome/regions/genelists" + input[1] = channel.fromPath(genelists_path + "/*.bed").collect().map{ files -> [ files ] }.ifEmpty { channel.empty() } + """ + } + } + + then { + assert workflow.success + assert snapshot(sanitizeOutput(workflow.out, unstableKeys:["riker_pdf"])).match() + } + + } + + test("bam QC - full - no roi") { + + when { + workflow { + """ + // [meta, bam, bai, roi, fasta, fai, gtf] + input[0] = Channel.of([ + [ id:'test', single_end:false, qc_mode:'full' ], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), + [], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf", checkIfExists: true) + ]) + // genelists + def genelists_path = "s3://test-data/genomics/homo_sapiens/genome/regions/genelists" + input[1] = channel.fromPath(genelists_path + "/*.bed").collect().map{ files -> [ files ] }.ifEmpty { channel.empty() } + """ + } + } + + then { + assert workflow.success + assert snapshot(sanitizeOutput(workflow.out, unstableKeys:["riker_pdf"])).match() + } + + } + + test("bam QC - basic - roi") { + + when { + workflow { + """ + // [meta, bam, bai, roi, fasta, fai, gtf] + input[0] = Channel.of([ + [ id:'test', single_end:false, qc_mode:'basic' ], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf", checkIfExists: true) + ]) + // genelists + def genelists_path = "s3://test-data/genomics/homo_sapiens/genome/regions/genelists" + input[1] = channel.fromPath(genelists_path + "/*.bed").collect().map{ files -> [ files ] }.ifEmpty { channel.empty() } + """ + } + } + + then { + assert workflow.success + assert snapshot(sanitizeOutput(workflow.out, unstableKeys:["riker_pdf"])).match() + } + + } + + test("bam QC - full - roi - WES") { + + when { + workflow { + """ + // [meta, bam, bai, roi, fasta, fai, gtf] + input[0] = Channel.of([ + [ id:'test', single_end:false, qc_mode:'full', tag:'WES' ], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf", checkIfExists: true) + ]) + // genelists + def genelists_path = "s3://test-data/genomics/homo_sapiens/genome/regions/genelists" + input[1] = channel.fromPath(genelists_path + "/*.bed").collect().map{ files -> [ files ] }.ifEmpty { channel.empty() } + """ + } + } + + then { + assert workflow.success + assert snapshot(sanitizeOutput(workflow.out, unstableKeys:["riker_pdf"])).match() + } + + } + + + test("bam QC - full - roi - seqcap") { + + when { + workflow { + """ + // [meta, bam, bai, roi, fasta, fai, gtf] + input[0] = Channel.of([ + [ id:'test', single_end:false, qc_mode:'full', tag:'seqcap' ], + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf", checkIfExists: true) + ]) + // genelists + def genelists_path = "s3://test-data/genomics/homo_sapiens/genome/regions/genelists" + input[1] = channel.fromPath(genelists_path + "/*.bed").collect().map{ files -> [ files ] }.ifEmpty { channel.empty() } + """ + } + } + + then { + assert workflow.success + assert snapshot(sanitizeOutput(workflow.out, unstableKeys:["riker_pdf"])).match() + } + + } +} diff --git a/subworkflows/local/bam_qc/tests/main.nf.test.snap b/subworkflows/local/bam_qc/tests/main.nf.test.snap new file mode 100644 index 00000000..e5a4f392 --- /dev/null +++ b/subworkflows/local/bam_qc/tests/main.nf.test.snap @@ -0,0 +1,1335 @@ +{ + "bam QC - basic - no roi": { + "content": [ + { + "mosdepth_global": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.mosdepth.global.dist.txt:md5,ceec5e216dac6a4e15b961713ee8b16c" + ] + ], + "mosdepth_per_base_bed": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.per-base.bed.gz:md5,c89a207273626f8415df1710bc522e8e" + ] + ], + "mosdepth_per_base_csi": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.per-base.bed.gz.csi:md5,c89ce701cf04e44aa49f54e2341c4bf0" + ] + ], + "mosdepth_per_base_d4": [ + + ], + "mosdepth_quantized_bed": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.quantized.bed.gz:md5,8975e3f5a62bb2ea6f349539daf8e9a4" + ] + ], + "mosdepth_quantized_csi": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.quantized.bed.gz.csi:md5,a4dd4f2635eaa215cc92ec03d754e955" + ] + ], + "mosdepth_regions": [ + + ], + "mosdepth_regions_bed": [ + + ], + "mosdepth_regions_csi": [ + + ], + "mosdepth_summary": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.mosdepth.summary.txt:md5,6c29875b821ba44f5cc5254a2339db90" + ] + ], + "mosdepth_thresholds_bed": [ + + ], + "mosdepth_thresholds_csi": [ + + ], + 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{ + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.quantized.bed.gz.csi:md5,a4dd4f2635eaa215cc92ec03d754e955" + ] + ], + "mosdepth_regions": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.mosdepth.region.dist.txt:md5,baffaa91e753347fd44c2e6e0a618d1f" + ] + ], + "mosdepth_regions_bed": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.regions.bed.gz:md5,82848481047cda38748ec0409db8a669" + ] + ], + "mosdepth_regions_csi": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.regions.bed.gz.csi:md5,d128b1a1648ebc007d22b5c4a23663a6" + ] + ], + "mosdepth_summary": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.mosdepth.summary.txt:md5,c929389c608f49ca01d800fb5cc94bb9" + ] + ], + "mosdepth_thresholds_bed": [ + + ], + "mosdepth_thresholds_csi": [ + + ], + "panelcoverage": [ + + ], + "riker_alignment_metrics": [ + + ], + "riker_base_dist": [ + + ], + "riker_error_indel": [ + + ], + "riker_error_mismatch": [ + + ], + "riker_error_overlap": [ + + ], + "riker_gcbias_detail": [ + + ], + "riker_gcbias_summary": [ + + ], + "riker_hybcap_metrics": [ + + ], + "riker_hybcap_per_base": [ + + ], + "riker_hybcap_per_target": [ + + ], + "riker_isize_histogram": [ + + ], + "riker_isize_metrics": [ + + ], + "riker_mean_qual": [ + + ], + "riker_pdf": [ + + ], + "riker_qual_dist": [ + + ], + "riker_rna_biotype": [ + + ], + "riker_rna_insert_size": [ + + ], + "riker_rna_insert_size_histogram": [ + + ], + "riker_rna_metrics": [ + + ], + "riker_wgs_coverage": [ + + ], + "riker_wgs_metrics": [ + + ], + "samtools_coverage": [ + + ], + "samtools_flagstat": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.flagstat:md5,167e69b479663a15194ddf56cbc9e60e" + ] + ], + "samtools_idxstats": [ + [ + { + "id": "test", + "qc_mode": "basic", + "single_end": false + }, + "test.idxstats:md5,081d0431383fb7ea6b51b7077c6ec93c" + ] + ], + "samtools_stats": [ + + ] + } + ], + "timestamp": "2026-09-08T12:06:10.847868", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/coverage/main.nf b/subworkflows/local/coverage/main.nf deleted file mode 100644 index f2cc25a6..00000000 --- a/subworkflows/local/coverage/main.nf +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env nextflow - -// MODULES -include { MOSDEPTH } from "../../../modules/nf-core/mosdepth/main.nf" -include { SAMTOOLS_COVERAGE } from "../../../modules/nf-core/samtools/coverage/main" -include { PANELCOVERAGE } from "../../../modules/local/panelcoverage/main" - -workflow COVERAGE { - take: - ch_meta_cram_crai_fasta_fai_roi // channel: [mandatory] [meta, cram, crai, fasta, fai, roi] - ch_genelists // channel: [optional] [genelists] - - main: - MOSDEPTH( - ch_meta_cram_crai_fasta_fai_roi.map { meta, cram, crai, fasta, _fai, roi -> - return [meta, cram, crai, roi, fasta] - }, - ['NO_COVERAGE', 'LOW_COVERAGE', 'CALLABLE'] - ) - - SAMTOOLS_COVERAGE( - ch_meta_cram_crai_fasta_fai_roi.map { meta, cram, crai, fasta, fai, _roi -> - return [meta, cram, crai, fasta, fai] - } - ) - - PANELCOVERAGE( - MOSDEPTH.out.per_base_bed.join(MOSDEPTH.out.per_base_csi).combine(ch_genelists).map { meta, bed, index, genelists -> - // Because groovy typing sucks ass; apparently an array of 1 is automatically converted to a string... - if (genelists !instanceof List) { - genelists = [genelists] - } - def filtered_genelists = meta.tag.toLowerCase() == "seqcap" - ? genelists.findAll { genelist -> genelist.name.toLowerCase().contains("seqcap") } - : genelists.findAll { genelist -> !genelist.name.toLowerCase().contains("seqcap") } - - if (filtered_genelists.size() > 0) { - return [ - meta, - bed, - index, - filtered_genelists, - ] - } - } - ) - - emit: - mosdepth_global = MOSDEPTH.out.global_txt - mosdepth_summary = MOSDEPTH.out.summary_txt - mosdepth_regions = MOSDEPTH.out.regions_txt - mosdepth_per_base_d4 = MOSDEPTH.out.per_base_d4 - mosdepth_per_base_bed = MOSDEPTH.out.per_base_bed - mosdepth_per_base_csi = MOSDEPTH.out.per_base_csi - mosdepth_regions_bed = MOSDEPTH.out.regions_bed - mosdepth_regions_csi = MOSDEPTH.out.regions_csi - mosdepth_quantized_bed = MOSDEPTH.out.quantized_bed - mosdepth_quantized_csi = MOSDEPTH.out.quantized_csi - mosdepth_thresholds_bed = MOSDEPTH.out.thresholds_bed - mosdepth_thresholds_csi = MOSDEPTH.out.thresholds_csi - samtools_coverage = SAMTOOLS_COVERAGE.out.coverage - panelcoverage = PANELCOVERAGE.out.regiondist -} diff --git a/subworkflows/local/coverage/meta.yml b/subworkflows/local/coverage/meta.yml deleted file mode 100644 index e69de29b..00000000 diff --git a/subworkflows/local/fastq_align_rna/main.nf b/subworkflows/local/fastq_align_rna/main.nf index d24c03b1..ef3f5c8c 100644 --- a/subworkflows/local/fastq_align_rna/main.nf +++ b/subworkflows/local/fastq_align_rna/main.nf @@ -41,9 +41,9 @@ workflow FASTQ_ALIGN_RNA { ) // Concatenate splice junction files - SORT_MERGE_SPLICE_JUNCTIONS(group_junctions(STAR_ALIGN.out.spl_junc_tab).map { meta, files -> [meta, files, "tab"]}) + SORT_MERGE_SPLICE_JUNCTIONS(group_junctions(STAR_ALIGN.out.spl_junc_tab).map { meta, files -> [meta, files, "tab"] }) // Concatenate junction files - SORT_MERGE_JUNCTIONS(group_junctions(STAR_ALIGN.out.junction).map { meta, files -> [meta, files, "junction"]}) + SORT_MERGE_JUNCTIONS(group_junctions(STAR_ALIGN.out.junction).map { meta, files -> [meta, files, "junction"] }) emit: bam = ch_bam // channel: [ [meta], bam ] diff --git a/subworkflows/local/fastq_align_rna/meta.yml b/subworkflows/local/fastq_align_rna/meta.yml index e69de29b..260c3d4d 100644 --- a/subworkflows/local/fastq_align_rna/meta.yml +++ b/subworkflows/local/fastq_align_rna/meta.yml @@ -0,0 +1,39 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "FASTQ_ALIGN_RNA" +description: Align RNA-seq FASTQ files with STAR and merge junction files +keywords: + - rna + - star + - alignment + - junctions +components: + - star/align + - gnu/sort +input: + - ch_reads_aligner_index_gtf: + type: file + description: | + Reads, aligner name, STAR index, and GTF. + + Structure: [ val(meta), path(reads), val(aligner), path(index), path(gtf) ] +output: + - bam: + type: file + description: | + Aligned BAM. + + Structure: [ val(meta), path(bam) ] + - splice_junctions: + type: file + description: Merged STAR splice junction table + - junctions: + type: file + description: Merged STAR junction file + - reports: + type: file + description: STAR log files +authors: + - "@matthdsm" +maintainers: + - "@matthdsm" + - "@nvnieuwk" diff --git a/tests/subworkflows/local/fastq_align_rna/main.nf.test b/subworkflows/local/fastq_align_rna/tests/main.nf.test similarity index 99% rename from tests/subworkflows/local/fastq_align_rna/main.nf.test rename to subworkflows/local/fastq_align_rna/tests/main.nf.test index c8319d20..44770cd7 100644 --- a/tests/subworkflows/local/fastq_align_rna/main.nf.test +++ b/subworkflows/local/fastq_align_rna/tests/main.nf.test @@ -39,7 +39,7 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:["bam", "reports", "junctions"]) + sanitizeOutput(workflow.out, unstableKeys:["bam","reports", "junctions"]) ).match() } diff --git a/tests/subworkflows/local/fastq_align_rna/main.nf.test.snap b/subworkflows/local/fastq_align_rna/tests/main.nf.test.snap similarity index 95% rename from tests/subworkflows/local/fastq_align_rna/main.nf.test.snap rename to subworkflows/local/fastq_align_rna/tests/main.nf.test.snap index f5e19b82..d3054b32 100644 --- a/tests/subworkflows/local/fastq_align_rna/main.nf.test.snap +++ b/subworkflows/local/fastq_align_rna/tests/main.nf.test.snap @@ -81,14 +81,14 @@ { "groupSize": 1, "groupTarget": { + "genome": { + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna" + }, "id": "test", - "samplename": "test", - "single_end": false, "sample_type": "RNA", - "genome": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai" - } + "samplename": "test", + "single_end": false } }, "test.SJ.out.tab:md5,15852c5678c04e86dcb66793b7e02bb9" @@ -96,10 +96,10 @@ ] } ], - "timestamp": "2026-05-14T08:11:34.101241", + "timestamp": "2026-09-16T16:06:51.009611", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.6" } }, "fastq align rna - unknown aligner": { diff --git a/subworkflows/local/fastq_to_aligned_cram/main.nf b/subworkflows/local/fastq_to_aligned_cram/main.nf index bf87f087..30a7f2cb 100644 --- a/subworkflows/local/fastq_to_aligned_cram/main.nf +++ b/subworkflows/local/fastq_to_aligned_cram/main.nf @@ -5,17 +5,18 @@ // // MODULES -include { BIOBAMBAM_BAMSORMADUP } from "../../../modules/nf-core/biobambam/bamsormadup/main.nf" -include { SAMTOOLS_CONVERT } from "../../../modules/nf-core/samtools/convert/main" -include { SAMTOOLS_SORMADUP } from "../../../modules/nf-core/samtools/sormadup/main.nf" -include { SAMTOOLS_SORT } from "../../../modules/nf-core/samtools/sort/main" +include { BIOBAMBAM_BAMSORMADUP } from "../../../modules/nf-core/biobambam/bamsormadup/main.nf" +include { SAMTOOLS_CONVERT } from "../../../modules/nf-core/samtools/convert/main" +include { SAMTOOLS_SORMADUP } from "../../../modules/nf-core/samtools/sormadup/main.nf" +include { SAMTOOLS_SORT } from "../../../modules/nf-core/samtools/sort/main" // SUBWORKFLOWS -include { FASTQ_ALIGN_DNA } from '../../nf-core/fastq_align_dna/main' -include { FASTQ_ALIGN_RNA } from '../../local/fastq_align_rna/main' +include { FASTQ_ALIGN_DNA } from '../../nf-core/fastq_align_dna/main' +include { FASTQ_ALIGN_RNA } from '../../local/fastq_align_rna/main' +include { FASTQ_UMICONSENSUS_FGUMI } from '../fastq_umiconsensus_fgumi/main.nf' // FUNCTIONS -include { getGenomeAttribute } from '../../local/utils_nfcore_preprocessing_pipeline' +include { getGenomeAttribute } from '../../local/utils_nfcore_preprocessing_pipeline' workflow FASTQ_TO_CRAM { take: @@ -35,6 +36,8 @@ workflow FASTQ_TO_CRAM { .branch { meta, reads, aligner, index, fasta, fai, gtf -> rna: meta.sample_type == "RNA" return [meta, reads, "star", getGenomeAttribute(meta.genome_data, 'star'), gtf] + umi: meta.call_consensus == true + return [meta, reads] dna: true // catch all non-RNA samples as DNA, as some may be missing sample_type or have other sample types (e.g. tissue, cell line, etc.) that should be aligned with the DNA aligner //dna: meta.sample_type == "DNA" || meta.sample_type == "Tissue" @@ -44,6 +47,9 @@ workflow FASTQ_TO_CRAM { // align fastq files per sample // ALIGNMENT([meta,fastq], index, sort) + FASTQ_UMICONSENSUS_FGUMI( + ch_meta_reads_aligner_index_fasta_datatype.umi + ) FASTQ_ALIGN_DNA( ch_meta_reads_aligner_index_fasta_datatype.dna, false, @@ -124,6 +130,7 @@ workflow FASTQ_TO_CRAM { */ ch_markdup_index + .mix(FASTQ_UMICONSENSUS_FGUMI.out.bam) .branch { meta, reads, index -> bam: reads.getExtension() == "bam" return [meta, reads, index] @@ -148,9 +155,10 @@ workflow FASTQ_TO_CRAM { ch_cram_crai.dump(tag: "FASTQ_TO_CRAM: cram and crai", pretty: true) emit: - cram_crai = ch_cram_crai - rna_splice_junctions = FASTQ_ALIGN_RNA.out.splice_junctions - rna_junctions = FASTQ_ALIGN_RNA.out.junctions - sormadup_metrics = ch_sormadup_metrics - align_reports = FASTQ_ALIGN_DNA.out.reports + cram_crai = ch_cram_crai + rna_splice_junctions = FASTQ_ALIGN_RNA.out.splice_junctions + rna_junctions = FASTQ_ALIGN_RNA.out.junctions + sormadup_metrics = ch_sormadup_metrics + align_reports = FASTQ_ALIGN_DNA.out.reports + family_size_histogram = FASTQ_UMICONSENSUS_FGUMI.out.family_size_histogram } diff --git a/subworkflows/local/fastq_to_aligned_cram/meta.yml b/subworkflows/local/fastq_to_aligned_cram/meta.yml index e69de29b..65157832 100644 --- a/subworkflows/local/fastq_to_aligned_cram/meta.yml +++ b/subworkflows/local/fastq_to_aligned_cram/meta.yml @@ -0,0 +1,51 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "FASTQ_TO_CRAM" +description: Align FASTQ files, mark duplicates, and convert to CRAM +keywords: + - fastq + - alignment + - markdup + - cram +components: + - biobambam/bamsormadup + - samtools/convert + - samtools/sormadup + - samtools/sort + - fastq_align_dna + - fastq_align_rna + - fastq_umiconsensus_fgumi + - getgenomeattribute +input: + - ch_meta_reads_aligner_index_fasta_fai_gtf: + type: file + description: | + Reads, aligner, index, and references. + + Structure: [ val(meta), path(reads), val(aligner), path(index), path(fasta), path(fai), path(gtf) ] +output: + - cram_crai: + type: file + description: | + CRAM and index. + + Structure: [ val(meta), path(cram), path(crai) ] + - rna_splice_junctions: + type: file + description: STAR splice junctions + - rna_junctions: + type: file + description: STAR junctions + - sormadup_metrics: + type: file + description: Duplicate metrics + - align_reports: + type: file + description: Aligner's report files + - family_size_histogram: + type: file + description: UMI family size histogram from fgumi +authors: + - "@matthdsm" +maintainers: + - "@matthdsm" + - "@nvnieuwk" diff --git a/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test b/subworkflows/local/fastq_to_aligned_cram/tests/main.nf.test similarity index 75% rename from tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test rename to subworkflows/local/fastq_to_aligned_cram/tests/main.nf.test index f3082fc3..312bce68 100644 --- a/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test +++ b/subworkflows/local/fastq_to_aligned_cram/tests/main.nf.test @@ -44,7 +44,10 @@ nextflow_workflow { { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:["cram_crai"]) + sanitizeOutput( + workflow.out, + unstableKeys:["cram_crai"] + ) ).match() } ) @@ -88,7 +91,10 @@ nextflow_workflow { { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:["cram_crai","rna_junctions"]) + sanitizeOutput( + workflow.out, + unstableKeys:["cram_crai", "rna_junctions"] + ) ).match() } ) @@ -131,7 +137,10 @@ nextflow_workflow { { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:["cram_crai"]) + sanitizeOutput( + workflow.out, + unstableKeys:["cram_crai"], + ) ).match() } ) @@ -174,7 +183,64 @@ nextflow_workflow { { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:["cram_crai"]) + sanitizeOutput( + workflow.out, + unstableKeys:["cram_crai"] + ) + ).match() + } + ) + } + } + + test("fastq to cram - umi") { + when { + workflow { + """ + // [meta, [fq_1,fq_2], aligner, index, fasta] + input[0] = Channel.of([ + [ + id: "test", + samplename: "test", + single_end: false, + sample_type: "DNA", + markdup: "false", + call_consensus: true, + fgumi_extract_mode: "read_structures", + fgumi_read_structure_r1: "3M3S+T", + fgumi_read_structure_r2: "+T", + fgumi_simplex_min_reads: 1, + fgumi_snap_ignore_mismatched_pairs: false, + genome_data: [ + snap: "s3://test-data/genomics/homo_sapiens/genome/snap/", + fasta: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + fai: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + dict: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict" + ] + ], // meta map + [ + file("https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/sample1_S31_R1_001.fastq.gz", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/sample1_S31_R2_001.fastq.gz", checkIfExists: true) + ], + "snap", // aligner + file("s3://test-data/genomics/homo_sapiens/genome/snap/", checkIfExists: true), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna"), + file("s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai"), + [] + ]) + """ + } + } + + then { + assertAll( + { + assert workflow.success + assert snapshot( + sanitizeOutput( + workflow.out, + unstableKeys:["cram_crai"], + ) ).match() } ) @@ -218,7 +284,7 @@ nextflow_workflow { { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:["cram_crai"]) + sanitizeOutput(workflow.out, unstableKeys:["cram_crai"],) ).match() } ) diff --git a/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test.snap b/subworkflows/local/fastq_to_aligned_cram/tests/main.nf.test.snap similarity index 75% rename from tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test.snap rename to subworkflows/local/fastq_to_aligned_cram/tests/main.nf.test.snap index a4452c59..c68157ae 100644 --- a/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test.snap +++ b/subworkflows/local/fastq_to_aligned_cram/tests/main.nf.test.snap @@ -24,6 +24,9 @@ "test.merged.cram", "test.merged.cram.crai" ] + ], + "family_size_histogram": [ + ], "rna_junctions": [ @@ -36,10 +39,10 @@ ] } ], - "timestamp": "2026-02-11T20:19:51.825749", + "timestamp": "2026-09-10T09:14:13.546181", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "fastq to cram - bwa - bamsormadup": { @@ -67,6 +70,9 @@ "test.cram", "test.cram.crai" ] + ], + "family_size_histogram": [ + ], "rna_junctions": [ @@ -79,26 +85,26 @@ { "groupSize": 1, "groupTarget": { + "genome_data": { + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna" + }, "id": "test", - "samplename": "test", - "single_end": false, - "sample_type": "DNA", "markdup": "bamsormadup", - "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai" - } + "sample_type": "DNA", + "samplename": "test", + "single_end": false } }, - "test.merged.metrics.txt:md5,4ee20f12cb4d6077479a08310c8f6c70" + "test.merged.metrics.txt:md5,389dc2da2dd448c54dadd8c3fa110dc5" ] ] } ], - "timestamp": "2026-02-11T20:10:31.616836", + "timestamp": "2026-09-09T14:17:49.889335", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "fastq to cram - bwa - samtools sormadup": { @@ -126,6 +132,9 @@ "test.merged.cram", "test.merged.cram.crai" ] + ], + "family_size_histogram": [ + ], "rna_junctions": [ @@ -138,26 +147,26 @@ { "groupSize": 1, "groupTarget": { + "genome_data": { + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna" + }, "id": "test", - "samplename": "test", - "single_end": false, - "sample_type": "DNA", "markdup": "samtools", - "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai" - } + "sample_type": "DNA", + "samplename": "test", + "single_end": false } }, - "test.merged.metrics:md5,795c73aa836eb480e418f52db98e37cc" + "test.merged.metrics:md5,c4de8e394bb7110b952b2f42af335484" ] ] } ], - "timestamp": "2026-02-11T20:15:15.495706", + "timestamp": "2026-09-09T14:10:49.27252", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "fastq to cram - star - bamsormadup": { @@ -186,6 +195,9 @@ "test.cram", "test.cram.crai" ] + ], + "family_size_histogram": [ + ], "rna_junctions": [ [ @@ -212,16 +224,16 @@ { "groupSize": 1, "groupTarget": { - "id": "test", - "samplename": "test", - "single_end": false, - "sample_type": "RNA", - "markdup": "bamsormadup", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "star": "s3://test-data/genomics/homo_sapiens/genome/star/" - } + }, + "id": "test", + "markdup": "bamsormadup", + "sample_type": "RNA", + "samplename": "test", + "single_end": false } }, "test.SJ.out.tab:md5,15852c5678c04e86dcb66793b7e02bb9" @@ -232,16 +244,16 @@ { "groupSize": 1, "groupTarget": { - "id": "test", - "samplename": "test", - "single_end": false, - "sample_type": "RNA", - "markdup": "bamsormadup", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "star": "s3://test-data/genomics/homo_sapiens/genome/star/" - } + }, + "id": "test", + "markdup": "bamsormadup", + "sample_type": "RNA", + "samplename": "test", + "single_end": false } }, "test.merged.metrics.txt:md5,641527401576375d7c0b0b54fbaf63ab" @@ -249,10 +261,10 @@ ] } ], - "timestamp": "2026-05-14T08:18:36.857986", + "timestamp": "2026-09-09T14:19:41.853779", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.6" } }, "fastq to cram - bwa - samtools sort": { @@ -281,6 +293,62 @@ "test.merged.cram.crai" ] ], + "family_size_histogram": [ + + ], + "rna_junctions": [ + + ], + "rna_splice_junctions": [ + + ], + "sormadup_metrics": [ + + ] + } + ], + "timestamp": "2026-07-03T10:48:56.909948371", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } + }, + "fastq to cram - umi": { + "content": [ + { + "align_reports": [ + + ], + "cram_crai": [ + + ], + "family_size_histogram": [ + [ + { + "groupSize": 1, + "groupTarget": { + "call_consensus": true, + "fgumi_extract_mode": "read_structures", + "fgumi_read_structure_r1": "3M3S+T", + "fgumi_read_structure_r2": "+T", + "fgumi_simplex_min_reads": 1, + "fgumi_snap_ignore_mismatched_pairs": false, + "genome_data": { + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "snap": "s3://test-data/genomics/homo_sapiens/genome/snap/" + }, + "id": "test", + "markdup": "false", + "sample_type": "DNA", + "samplename": "test", + "single_end": false + } + }, + "test.fgumi.group.family_size_histogram.txt:md5,c0a94c347cb92494ce84b1cdb09fca10" + ] + ], "rna_junctions": [ ], @@ -292,10 +360,10 @@ ] } ], - "timestamp": "2026-02-11T20:16:26.285299", + "timestamp": "2026-09-16T20:07:14.849842", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/subworkflows/local/fastq_umiconsensus_fgumi/main.nf b/subworkflows/local/fastq_umiconsensus_fgumi/main.nf new file mode 100644 index 00000000..0391bd4f --- /dev/null +++ b/subworkflows/local/fastq_umiconsensus_fgumi/main.nf @@ -0,0 +1,95 @@ +#!/usr/bin/env nextflow + +// MODULES +include { FGUMI_EXTRACTSORT } from "../../../modules/local/fgumi/extractsort/main.nf" +include { FGUMI_FILTER } from "../../../modules/nf-core/fgumi/filter/main.nf" +include { FGUMI_GROUP } from "../../../modules/nf-core/fgumi/group/main.nf" +include { FGUMI_MERGE } from "../../../modules/nf-core/fgumi/merge/main.nf" +include { FGUMI_SIMPLEX } from "../../../modules/nf-core/fgumi/simplex/main.nf" +include { FGUMI_SNAPZIPSORT as RAW_FGUMI_SNAPZIPSORT } from "../../../modules/local/fgumi/snapzipsort/main.nf" +include { FGUMI_SNAPZIPSORT as UMI_FGUMI_SNAPZIPSORT } from "../../../modules/local/fgumi/snapzipsort/main.nf" + + +// FUNCTIONS +include { getGenomeAttribute } from '../../local/utils_nfcore_preprocessing_pipeline' + +workflow FASTQ_UMICONSENSUS_FGUMI { + take: + ch_meta_fastqs // channel: [mandatory] [meta, fastqs] + + main: + // Step numbers follow the fgumi basic workflow terminology (this path executes steps 1, 3, 4, 5, and 7). + // Step 1: build an unmapped BAM with UMI tags from input FASTQ. + FGUMI_EXTRACTSORT( + ch_meta_fastqs.map { meta, fastqs -> [meta, fastqs, (meta.readgroup?.LB ?: meta.library ?: meta.id)] } + ) + + // Step 3: align with SNAP, zipper tags back, then template-coordinate sort. + RAW_FGUMI_SNAPZIPSORT( + FGUMI_EXTRACTSORT.out.bam.map { meta, ubams -> + [meta, ubams, getGenomeAttribute(meta.genome_data, 'snap'), getGenomeAttribute(meta.genome_data, 'fasta'), getGenomeAttribute(meta.genome_data, 'fai'), getGenomeAttribute(meta.genome_data, 'dict')] + } + ) + + def ch_merge_input = RAW_FGUMI_SNAPZIPSORT.out.bam + .map { meta, files -> + def gk = (meta.chunks as Integer ?: 1) + return [ + groupKey( + meta - meta.subMap('readgroup', 'chunks') + [id: meta.id ==~ /^\d{4}\..*$/ ? meta.id[5..-1] : meta.id], + gk, + ), + files, + ] + } + .groupTuple() + .map { meta, files -> + def gk = (meta.count as Integer ?: 1) + return [ + groupKey( + meta - meta.subMap('count') + [id: meta.samplename ?: meta.id], + gk, + ), + files, + ] + } + .groupTuple() + .map { meta, files -> + return [meta, files.flatten()] + } + + FGUMI_MERGE( + ch_merge_input + ) + + FGUMI_GROUP( + FGUMI_MERGE.out.bam, + 'adjacency', + ) + + FGUMI_SIMPLEX( + FGUMI_GROUP.out.bam.map { meta, bams -> [meta, bams, meta.fgumi_simplex_min_reads, false] } + ) + + // Step 7: filter consensus reads, then coordinate-sort/index for downstream CRAM conversion. + FGUMI_FILTER( + FGUMI_SIMPLEX.out.bam.map { meta, simplex_bams -> + [meta, simplex_bams, getGenomeAttribute(meta.genome_data, 'fasta')] + }, + '1,1,1', + false, + ) + + UMI_FGUMI_SNAPZIPSORT( + FGUMI_FILTER.out.bam.map { meta, filtered_bams -> + [meta, filtered_bams, getGenomeAttribute(meta.genome_data, 'snap'), getGenomeAttribute(meta.genome_data, 'fasta'), getGenomeAttribute(meta.genome_data, 'fai'), getGenomeAttribute(meta.genome_data, 'dict')] + } + ) + + emit: + bam = UMI_FGUMI_SNAPZIPSORT.out.bam.join(UMI_FGUMI_SNAPZIPSORT.out.bai) + grouping_metrics = FGUMI_GROUP.out.metrics + family_size_histogram = FGUMI_GROUP.out.histogram + consensus_metrics = FGUMI_SIMPLEX.out.stats + filtering_metrics = FGUMI_FILTER.out.stats +} diff --git a/subworkflows/local/fastq_umiconsensus_fgumi/meta.yml b/subworkflows/local/fastq_umiconsensus_fgumi/meta.yml new file mode 100644 index 00000000..9fb4b3fd --- /dev/null +++ b/subworkflows/local/fastq_umiconsensus_fgumi/meta.yml @@ -0,0 +1,47 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "FASTQ_UMICONSENSUS_FGUMI" +description: Extract UMIs, consensus-call with fgumi, and SNAP-align +keywords: + - umi + - fgumi + - snap + - consensus +components: + - fgumi/extract + - fgumi/filter + - fgumi/group + - fgumi/merge + - fgumi/simplex + - fgumi/snapzipsort + - getgenomeattribute +input: + - ch_meta_fastqs: + type: file + description: | + FASTQ files for UMI consensus. + + Structure: [ val(meta), path(fastqs) ] +output: + - bam: + type: file + description: | + Coordinate-sorted BAM and index. + + Structure: [ val(meta), path(bam), path(bai) ] + - grouping_metrics: + type: file + description: fgumi group metrics + - family_size_histogram: + type: file + description: UMI family size histogram + - consensus_metrics: + type: file + description: fgumi simplex stats + - filtering_metrics: + type: file + description: fgumi filter stats +authors: + - "@matthdsm" +maintainers: + - "@matthdsm" + - "@nvnieuwk" diff --git a/subworkflows/local/fastq_umiconsensus_fgumi/tests/main.nf.test b/subworkflows/local/fastq_umiconsensus_fgumi/tests/main.nf.test new file mode 100644 index 00000000..36cb5068 --- /dev/null +++ b/subworkflows/local/fastq_umiconsensus_fgumi/tests/main.nf.test @@ -0,0 +1,67 @@ +nextflow_workflow { + + name "Test Workflow FASTQ_UMICONSENSUS_FGUMI" + script "subworkflows/local/fastq_umiconsensus_fgumi/main.nf" + workflow "FASTQ_UMICONSENSUS_FGUMI" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows/local" + tag "subworkflows/local/fastq_umiconsensus_fgumi" + + test("umi consensus test") { + when { + workflow { + """ + // [meta, [fq_1,fq_2]] + input[0] = channel.of([ + [ + id:'test', + readgroup: [ + ID: "test", + LB: "lib1", + PL: "ILLUMINA", + PU: "unit1", + PM: "model1", + CN: "center1", + PI: 300, + DS: "description", + DT: "2024-06-01" + ], + samplename:'test', + single_end:false, + sample_type:'DNA', + markdup: "false", + fgumi_extract_mode: "read_structures", + fgumi_read_structure_r1: "3M3S+T", + fgumi_read_structure_r2: "+T", + fgumi_simplex_min_reads: 1, + fgumi_snap_ignore_mismatched_pairs: false, + genome_data: [ + snap: "s3://test-data/genomics/homo_sapiens/genome/snap/", + fasta: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + fai: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + dict: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict" + ] + ], // meta map + [ + file("https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/sample1_S31_R1_001.fastq.gz", checkIfExists: true), + file("https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/sample1_S31_R2_001.fastq.gz", checkIfExists: true) + ] + ]) + """ + } + } + + then { + assertAll( + { + assert workflow.success + assert snapshot( + sanitizeOutput(workflow.out, unstableKeys:["bam"]) + ).match() + } + ) + } + } +} diff --git a/subworkflows/local/fastq_umiconsensus_fgumi/tests/main.nf.test.snap b/subworkflows/local/fastq_umiconsensus_fgumi/tests/main.nf.test.snap new file mode 100644 index 00000000..f0f454bd --- /dev/null +++ b/subworkflows/local/fastq_umiconsensus_fgumi/tests/main.nf.test.snap @@ -0,0 +1,120 @@ +{ + "umi consensus test": { + "content": [ + { + "bam": [ + + ], + "consensus_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "fgumi_extract_mode": "read_structures", + "fgumi_read_structure_r1": "3M3S+T", + "fgumi_read_structure_r2": "+T", + "fgumi_simplex_min_reads": 1, + "fgumi_snap_ignore_mismatched_pairs": false, + "genome_data": { + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "snap": "s3://test-data/genomics/homo_sapiens/genome/snap/" + }, + "id": "test", + "markdup": "false", + "sample_type": "DNA", + "samplename": "test", + "single_end": false + } + }, + "test.fgumi.simplex.stats.txt:md5,ba5e755a7459c96e1f358e18f32e174c" + ] + ], + "family_size_histogram": [ + [ + { + "groupSize": 1, + "groupTarget": { + "fgumi_extract_mode": "read_structures", + "fgumi_read_structure_r1": "3M3S+T", + "fgumi_read_structure_r2": "+T", + "fgumi_simplex_min_reads": 1, + "fgumi_snap_ignore_mismatched_pairs": false, + "genome_data": { + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "snap": "s3://test-data/genomics/homo_sapiens/genome/snap/" + }, + "id": "test", + "markdup": "false", + "sample_type": "DNA", + "samplename": "test", + "single_end": false + } + }, + "test.fgumi.group.family_size_histogram.txt:md5,c0a94c347cb92494ce84b1cdb09fca10" + ] + ], + "filtering_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "fgumi_extract_mode": "read_structures", + "fgumi_read_structure_r1": "3M3S+T", + "fgumi_read_structure_r2": "+T", + "fgumi_simplex_min_reads": 1, + "fgumi_snap_ignore_mismatched_pairs": false, + "genome_data": { + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "snap": "s3://test-data/genomics/homo_sapiens/genome/snap/" + }, + "id": "test", + "markdup": "false", + "sample_type": "DNA", + "samplename": "test", + "single_end": false + } + }, + "test.fgumi.filter.stats.txt:md5,562a544db15f3953dd1f6dc61d44db76" + ] + ], + "grouping_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "fgumi_extract_mode": "read_structures", + "fgumi_read_structure_r1": "3M3S+T", + "fgumi_read_structure_r2": "+T", + "fgumi_simplex_min_reads": 1, + "fgumi_snap_ignore_mismatched_pairs": false, + "genome_data": { + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "snap": "s3://test-data/genomics/homo_sapiens/genome/snap/" + }, + "id": "test", + "markdup": "false", + "sample_type": "DNA", + "samplename": "test", + "single_end": false + } + }, + "test.fgumi.group.grouping_metrics.txt:md5,f624f39fc4b0f257f5933a9250dfddd0" + ] + ] + } + ], + "timestamp": "2026-09-16T15:47:47.748945", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/fastq_umiconsensus_fgumi/tests/nextflow.config b/subworkflows/local/fastq_umiconsensus_fgumi/tests/nextflow.config new file mode 100644 index 00000000..7c4f47f0 --- /dev/null +++ b/subworkflows/local/fastq_umiconsensus_fgumi/tests/nextflow.config @@ -0,0 +1,59 @@ +process { + withName: FGUMI_EXTRACTSORT { + ext.prefix = { "${meta.id}.fgumi.unmapped" } + ext.args = { + [ + "--read-group-id ${meta.readgroup?.get('ID') ? meta.readgroup.get('ID') : meta.id}", + meta.fgumi_extract_mode == "read_names" ? "--extract-umis-from-read-names" : "", + meta.fgumi_extract_mode == "read_structures" ? "--read-structures ${meta.fgumi_read_structure_r1} ${meta.fgumi_read_structure_r2}" : "", + ].join(" ").trim() + } + ext.args2 = { + ["--order queryname::natural"].join(" ").trim() + } + } + withName: RAW_FGUMI_SNAPZIPSORT { + // SNAP + ext.args = "" + // Initial Sort + ext.args2 = { + [ + "--order queryname::natural", + "--compression-level 0", + ].join(" ").trim() + } + // Zipper + ext.args3 = { + ["--compression-level 0"].join(" ").trim() + } + // Final Sort + ext.args4 = { + [ + "--order template-coordinate", + "--key-types mi", + ].join(" ").trim() + } + } + withName: UMI_FGUMI_SNAPZIPSORT { + // SNAP + ext.args = "" + // Initial Sort + ext.args2 = { + [ + "--order queryname::natural", + "--compression-level 0", + ].join(" ").trim() + } + // Zipper + ext.args3 = { + ["--compression-level 0"].join(" ").trim() + } + // Final Sort + ext.args4 = { + [ + "--order coordinate", + "--key-types mi", + ].join(" ").trim() + } + } +} diff --git a/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/main.nf b/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/main.nf index a20d0849..71a8e13c 100644 --- a/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/main.nf +++ b/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/main.nf @@ -4,8 +4,13 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Mock subworkflow to please linting workflow UTILS_NFCMGG_PREPROCESSING_PIPELINE { + + main: + dummy_emit = true + + emit: + dummy_emit } /* @@ -34,10 +39,14 @@ def getReadgroupFromFastq(fastq, SM, LB, CN) { line = line.substring(1) def fields = line.split(':') def rg = [:] - rg.LB = LB ?: '' - rg.CN = CN ?: '' rg.PL = 'ILLUMINA' rg.SM = SM ?: fastq.name.toString() - ~/_R[0-9]_001.*$/ + if (LB) { + rg.LB = LB + } + if (CN) { + rg.CN = CN + } if (fields.size() >= 7) { // CASAVA 1.8+ format, from https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm // "@::::::: :::" @@ -77,11 +86,16 @@ def getReadgroupsFromBclconvert(ch_fastq_list_csv, ch_fastq) { // RGPU is a custom column in the samplesheet containing the flowcell ID rg.PU = row.RGPU ? row.RGPU : meta.id + "." + row.Lane rg.SM = row.RGSM - rg.LB = row.RGLB ? row.RGLB : "" + if (row.RGLB) { + rg.LB = row.RGLB + } rg.PL = "ILLUMINA" // dereference the fastq files in the csv def fastq1 = fastq_list.find { fq -> file(fq).name == file(row.Read1File).name } + if (!fastq1) { + error("BCL Convert fastq_list.csv Read1File '${row.Read1File}' for sample '${row.RGSM}' was not in the demultiplexed FASTQs") + } def fastq2 = row.Read2File ? fastq_list.find { fq -> file(fq).name == file(row.Read2File).name } : null // set fastq metadata @@ -93,3 +107,46 @@ def getReadgroupsFromBclconvert(ch_fastq_list_csv, ch_fastq) { } .flatMap() } + +// +// Pick the sampleinfo row for a demultiplexed FASTQ. +// Sampleinfo is parsed once per flowcell lane, so identical rows repeat and are deduplicated. +// One row per samplename is attached as-is. Multiple rows require a unique +// match of sampleinfo.library to readgroup.LB. +// +def matchSampleinfo(meta, infos) { + def rows = (infos instanceof Collection ? infos as List : [infos]).unique(false) + if (rows.size() == 1) { + return rows[0] + } + def samplename = meta.readgroup?.SM ?: meta.samplename + def lb = meta.readgroup?.LB + def matches = rows.findAll { row -> row.library && lb && row.library == lb } + if (matches.size() != 1) { + error("Multiplexed sample '${samplename}' needs a unique sampleinfo row for library '${lb}'. Set Illumina LibraryName so BCL Convert RGLB matches sampleinfo.library.") + } + return matches[0] +} + +// +// Associate demultiplexed FASTQs [meta, fastq] with sampleinfo rows. +// +def associateSampleinfo(ch_fastq, ch_sampleinfo) { + def ch_info = ch_sampleinfo + .map { sampleinfo -> [sampleinfo.samplename, sampleinfo] } + .groupTuple() + return ch_fastq + .map { meta, fastq -> [meta.readgroup.SM, meta, fastq] } + .combine(ch_info, by: 0) + .map { _samplename, meta, fastq, infos -> + return [meta, fastq, matchSampleinfo(meta, infos)] + } +} + +// +// Output directory for a sample. Multiplexed libraries stay under library/samplename. +// +def samplePublishDir(meta) { + def samplename = meta.samplename ?: meta.id + return meta.library ? "${meta.library}/${samplename}" : "${samplename}" +} diff --git a/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/meta.yml b/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/meta.yml index e69de29b..c9bdbdad 100644 --- a/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/meta.yml +++ b/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/meta.yml @@ -0,0 +1,19 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCMGG_PREPROCESSING_PIPELINE" +description: Helper functions for nf-cmgg/preprocessing (readgroups, sampleinfo, publish paths) +keywords: + - utility + - readgroup + - sampleinfo + - preprocessing +components: [] +input: [] +output: + - dummy_emit: + type: boolean + description: Dummy emit +authors: + - "@matthdsm" +maintainers: + - "@matthdsm" + - "@nvnieuwk" diff --git a/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..d5fc11a8 --- /dev/null +++ b/subworkflows/local/utils_nfcmgg_preprocessing_pipeline/tests/main.function.nf.test @@ -0,0 +1,179 @@ +nextflow_function { + + name "Test Functions" + script "subworkflows/local/utils_nfcmgg_preprocessing_pipeline/main.nf" + tag "subworkflows" + tag "subworkflows/local" + tag "subworkflows/local/utils_nfcmgg_preprocessing_pipeline" + + test("Test Function matchSampleinfo - singleton") { + + function "matchSampleinfo" + + when { + function { + """ + input[0] = [readgroup: [SM: 'Sample1', LB: '']] + input[1] = [[samplename: 'Sample1', library: 'test', aligner: 'bwamem']] + """ + } + } + + then { + assert function.success + assert function.result.library == 'test' + assert function.result.aligner == 'bwamem' + } + } + + test("Test Function matchSampleinfo - multiplexed library") { + + function "matchSampleinfo" + + when { + function { + """ + input[0] = [readgroup: [SM: 'Sample1', LB: 'libB']] + input[1] = [ + [samplename: 'Sample1', library: 'libA', aligner: 'bwamem'], + [samplename: 'Sample1', library: 'libB', aligner: 'star'] + ] + """ + } + } + + then { + assert function.success + assert function.result.library == 'libB' + assert function.result.aligner == 'star' + } + } + + test("Test Function matchSampleinfo - singleton repeated per lane") { + + function "matchSampleinfo" + + when { + function { + """ + input[0] = [readgroup: [SM: 'Sample1', LB: 'libA']] + input[1] = [ + [samplename: 'Sample1', library: 'libA', aligner: 'bwamem'], + [samplename: 'Sample1', library: 'libA', aligner: 'bwamem'] + ] + """ + } + } + + then { + assert function.success + assert function.result.library == 'libA' + assert function.result.aligner == 'bwamem' + } + } + + test("Test Function matchSampleinfo - multiplexed repeated per lane") { + + function "matchSampleinfo" + + when { + function { + """ + input[0] = [readgroup: [SM: 'Sample1', LB: 'libB']] + input[1] = [ + [samplename: 'Sample1', library: 'libA', aligner: 'bwamem'], + [samplename: 'Sample1', library: 'libB', aligner: 'star'], + [samplename: 'Sample1', library: 'libA', aligner: 'bwamem'], + [samplename: 'Sample1', library: 'libB', aligner: 'star'] + ] + """ + } + } + + then { + assert function.success + assert function.result.library == 'libB' + assert function.result.aligner == 'star' + } + } + + test("Test Function matchSampleinfo - multiplexed missing RGLB") { + + function "matchSampleinfo" + + when { + function { + """ + input[0] = [readgroup: [SM: 'Sample1', LB: '']] + input[1] = [ + [samplename: 'Sample1', library: 'libA'], + [samplename: 'Sample1', library: 'libB'] + ] + """ + } + } + + then { + assert !function.success + assert function.stdout.any { it.contains("Multiplexed sample 'Sample1'") } + } + } + + test("Test Function matchSampleinfo - multiplexed unmatched library") { + + function "matchSampleinfo" + + when { + function { + """ + input[0] = [readgroup: [SM: 'Sample1', LB: 'libC']] + input[1] = [ + [samplename: 'Sample1', library: 'libA'], + [samplename: 'Sample1', library: 'libB'] + ] + """ + } + } + + then { + assert !function.success + assert function.stdout.any { it.contains("library 'libC'") } + } + } + + test("Test Function samplePublishDir - multiplexed library") { + + function "samplePublishDir" + + when { + function { + """ + input[0] = [samplename: 'Sample1', library: 'libB'] + """ + } + } + + then { + assert function.success + assert function.result == 'libB/Sample1' + } + } + + test("Test Function samplePublishDir - no library") { + + function "samplePublishDir" + + when { + function { + """ + input[0] = [samplename: 'Sample1'] + """ + } + } + + then { + assert function.success + assert function.result == 'Sample1' + } + } +} diff --git a/subworkflows/local/utils_nfcore_preprocessing_pipeline/main.nf b/subworkflows/local/utils_nfcore_preprocessing_pipeline/main.nf index 2b44eaa0..8cb2c88e 100644 --- a/subworkflows/local/utils_nfcore_preprocessing_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_preprocessing_pipeline/main.nf @@ -11,7 +11,6 @@ include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' include { samplesheetToList } from 'plugin/nf-schema' -include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' @@ -27,6 +26,7 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet @@ -36,6 +36,8 @@ workflow PIPELINE_INITIALISATION { main: + ch_versions = channel.empty() + // // Print version and exit if required and dump pipeline parameters to JSON file // @@ -49,6 +51,13 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // + + def before_text = "" + def after_text = "" + if (monochrome_logs) { + before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '') + } + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " UTILS_NFSCHEMA_PLUGIN( @@ -58,10 +67,10 @@ workflow PIPELINE_INITIALISATION { help, help_full, show_hidden, - "", - "", + before_text, + after_text, command, - false + false, ) // @@ -79,11 +88,13 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - channel.fromList(samplesheetToList(input, "assets/schema_input.json")) + + channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) .set { ch_samplesheet } emit: samplesheet = ch_samplesheet + versions = ch_versions } /* @@ -102,7 +113,7 @@ workflow PIPELINE_COMPLETION { multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + summary_params = paramsSummaryMap(parameters_schema: "nextflow_schema.json") def multiqc_reports = multiqc_report.toList() // @@ -125,7 +136,7 @@ workflow PIPELINE_COMPLETION { } workflow.onError { - log.error("Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting") + log.error("Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting") } } @@ -138,7 +149,6 @@ workflow PIPELINE_COMPLETION { // Check and validate pipeline parameters // def validateInputParameters() { - genomeExistsError() } // @@ -162,7 +172,6 @@ def getGenomeAttribute(genomes, attribute) { if (genomes && genomes.containsKey(attribute)) { return genomes[attribute] } - return null } // @@ -178,12 +187,23 @@ def genomeExistsError() { // Generate methods description for MultiQC // def toolCitationText() { - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "FastQC (Andrews 2010),", + "BCL Convert,", + "fastp (Chen et al. 2018),", + "Falco (de Sena Brandine and Smith 2021),", + "BWA-MEM (Li 2013),", + "BWA-MEM2 (Vasimuddin et al. 2019),", + "Bowtie 2 (Langmead and Salzberg 2012),", + "DRAGMAP,", + "SNAP (Zaharia et al. 2011),", + "strobealign (Sahlin 2022),", + "STAR (Dobin et al. 2013),", + "fgumi,", + "biobambam2 (Tischler and Leonard 2014),", + "SAMtools (Li et al. 2009),", + "mosdepth (Pedersen and Quinlan 2018),", + "riker,", "MultiQC (Ewels et al. 2016)", ".", ].join(' ').trim() @@ -192,12 +212,19 @@ def toolCitationText() { } def toolBibliographyText() { - // TODO nf-core: Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • ", + "
  • Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560.
    • ", + "
  • de Sena Brandine G, Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Res. 2021 Jan 27;8:1874. doi: 10.12688/f1000research.21142.2.
    • ", + "
  • Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013. doi: 10.48550/arXiv.1303.3997.
    • ", + "
  • Vasimuddin M, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE IPDPS, pp. 314-324. doi: 10.1109/IPDPS.2019.00041.
    • ", + "
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.
    • ", + "
  • Zaharia M, et al. Faster and More Accurate Sequence Alignment with SNAP. arXiv 2011. doi: 10.48550/arXiv.1111.5572.
    • ", + "
  • Sahlin K. Strobealign: flexible seed size enables ultra-fast and accurate read alignment. Genome Biol. 2022 Dec 29;23(1):260. doi: 10.1186/s13059-022-02831-7.
    • ", + "
  • Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635.
    • ", + "
  • Tischler G, Leonard S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol Med. 2014 Jun 20;9:13. doi: 10.1186/1751-0473-9-13.
    • ", + "
  • Li H, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352.
    • ", + "
  • Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699.
    • ", + "
  • Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354.
    • ", ].join(' ').trim() return reference_text @@ -226,13 +253,8 @@ def methodsDescriptionText(mqc_methods_yaml) { } meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - // meta["tool_bibliography"] = toolBibliographyText() + meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + meta["tool_bibliography"] = toolBibliographyText() def methods_text = mqc_methods_yaml.text diff --git a/subworkflows/local/utils_nfcore_preprocessing_pipeline/meta.yml b/subworkflows/local/utils_nfcore_preprocessing_pipeline/meta.yml index e69de29b..9dc59294 100644 --- a/subworkflows/local/utils_nfcore_preprocessing_pipeline/meta.yml +++ b/subworkflows/local/utils_nfcore_preprocessing_pipeline/meta.yml @@ -0,0 +1,54 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "PIPELINE_INITIALISATION" +description: Initialise and complete nf-cmgg/preprocessing runs +keywords: + - utility + - pipeline + - initialise + - samplesheet +components: + - utils_nfschema_plugin + - utils_nfcore_pipeline + - utils_nextflow_pipeline + - completionemail + - completionsummary +input: + - version: + type: boolean + description: Print the pipeline version and exit + - validate_params: + type: boolean + description: Validate pipeline parameters against the schema + - monochrome_logs: + type: boolean + description: Disable coloured log output + - nextflow_cli_args: + type: list + description: Nextflow CLI positional arguments + - outdir: + type: directory + description: Pipeline results directory + - input: + type: file + description: Samplesheet path + - help: + type: boolean + description: Show the help message and exit + - help_full: + type: boolean + description: Show the full help message and exit + - show_hidden: + type: boolean + description: Show hidden parameters in the help message +output: + - samplesheet: + type: map + description: Channel of samplesheet rows + - versions: + type: file + description: Software versions collected during initialisation +authors: + - "@matthdsm" +maintainers: + - "@matthdsm" + - "@nvnieuwk" diff --git a/subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff b/subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff index 2055abd1..05d43902 100644 --- a/subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff +++ b/subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff @@ -15,7 +15,7 @@ Changes in 'fastq_align_dna/main.nf': sort // boolean: [mandatory] true -> sort, false -> don't sort main: -@@ -28,45 +25,52 @@ +@@ -28,45 +25,54 @@ ch_bam = channel.empty() ch_reports = channel.empty() @@ -38,9 +38,11 @@ Changes in 'fastq_align_dna/main.nf': + .set { ch_to_align } + + // Throw error for all samples with unsupported aligners -+ ch_to_align.other.map { meta, _reads, aligner, _index, _fasta -> -+ error("Unsupported aligner ${aligner} for sample ${meta.id}") -+ } ++ ch_bam = ch_bam.mix( ++ ch_to_align.other.map { meta, _reads, aligner, _index, _fasta, _fai -> ++ error("Unsupported aligner ${aligner} for sample ${meta.id}") ++ } ++ ) + // Align fastq files to reference genome and (optionally) sort - if (aligner == 'bowtie2') { diff --git a/subworkflows/nf-core/fastq_align_dna/main.nf b/subworkflows/nf-core/fastq_align_dna/main.nf index af083220..e34e40f5 100644 --- a/subworkflows/nf-core/fastq_align_dna/main.nf +++ b/subworkflows/nf-core/fastq_align_dna/main.nf @@ -44,9 +44,11 @@ workflow FASTQ_ALIGN_DNA { .set { ch_to_align } // Throw error for all samples with unsupported aligners - ch_to_align.other.map { meta, _reads, aligner, _index, _fasta -> - error("Unsupported aligner ${aligner} for sample ${meta.id}") - } + ch_bam = ch_bam.mix( + ch_to_align.other.map { meta, _reads, aligner, _index, _fasta, _fai -> + error("Unsupported aligner ${aligner} for sample ${meta.id}") + } + ) // Align fastq files to reference genome and (optionally) sort BOWTIE2_ALIGN(ch_to_align.bowtie2, false, sort) diff --git a/subworkflows/nf-core/fastq_align_dna/meta.yml b/subworkflows/nf-core/fastq_align_dna/meta.yml index 26c3e237..b9506e15 100644 --- a/subworkflows/nf-core/fastq_align_dna/meta.yml +++ b/subworkflows/nf-core/fastq_align_dna/meta.yml @@ -18,33 +18,25 @@ components: - snapaligner/align - strobealign input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - reads: + - ch_reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - - meta2: - type: map + + Structure: [ val(meta), [ path(reads) ] ] + - ch_aligner_index: + type: directory description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - index: + Directory containing the aligner genome index files. + + Structure: [ val(meta2), path(index) ] + - ch_fasta: type: file - description: Aligner genome index files - pattern: "Directory containing aligner index" - - meta3: - type: map description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome in fasta format + Reference genome in fasta format. + + Structure: [ val(meta3), path(fasta) ] pattern: "*.{fa, fasta, fna}" - aligner: type: string @@ -56,31 +48,30 @@ input: - dragmap - snap - strobealign - - sort_bam: + - sort: type: boolean description: sort output output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - bam: type: file - description: BAM file + description: | + BAM file. + + Structure: [ val(meta), path(bam) ] pattern: "*.bam" - bam_index: type: file - description: BAM index (currently only for snapaligner) + description: | + BAM index (only produced by some aligners). + + Structure: [ val(meta), path(bai/csi) ] pattern: "*.{bai, csi}" - - report: - type: file - description: Alignment report (currently only for dragmap) - pattern: "*.txt" - - versions: + - reports: type: file - description: File containing software versions - pattern: "versions.yml" + description: | + Alignment report (currently only for dragmap). + + Structure: [ val(meta), path(log) ] authors: - "@matthdsm" maintainers: diff --git a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test index 793245ea..254491da 100644 --- a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test @@ -56,9 +56,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - ).match() } + { assert snapshot(sanitizeOutput(workflow.out, unstableKeys:["bam", "bam_index"])).match() } ) } } @@ -92,9 +90,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - ).match() } + { assert snapshot(sanitizeOutput(workflow.out, unstableKeys:["bam", "bam_index"])).match() } ) } } @@ -124,12 +120,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - workflow.out.bam_index, - workflow.out.reports, - ).match() - } + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index"])).match() } ) } } @@ -159,12 +150,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - workflow.out.bam_index, - workflow.out.reports, - ).match() - } + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index"])).match() } ) } } @@ -194,12 +180,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - workflow.out.bam_index, - workflow.out.reports, - ).match() - } + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index"])).match() } ) } } @@ -229,12 +210,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - workflow.out.bam_index, - workflow.out.reports, - ).match() - } + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index"])).match() } ) } } @@ -264,10 +240,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - file(workflow.out.reports[0][1]).readLines().findAll { it.startsWith("decompHash") }, - ).match() } + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index", "reports"])).match() } ) } } @@ -297,10 +270,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot( - file(workflow.out.bam[0][1]).name, - file(workflow.out.reports[0][1]).readLines().findAll { it.startsWith("decompHash") }, - ).match() } + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index", "reports"])).match() } ) } } @@ -330,7 +300,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index"])).match() } ) } } @@ -360,7 +330,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"])).match() } ) } } @@ -380,7 +350,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index"])).match() } ) } } @@ -400,7 +370,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert snapshot(sanitizeOutput(workflow.out, readsMD5Keys:["bam"], unstableKeys:["bam_index"])).match() } ) } } diff --git a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap index f002d8a4..c9c13411 100644 --- a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap @@ -1,63 +1,72 @@ { "test_fastq_align_bwamem2_PE": { "content": [ - "test.bam", - [ - - ], - [ - - ] + { + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5Reads,af8628d9df18b2d3d4f6fd47ef2bb872" + ] + ], + "bam_index": [ + + ], + "reports": [ + + ] + } ], - "timestamp": "2026-02-18T14:49:11.253548", + "timestamp": "2026-08-25T14:46:58.945883", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "test_fastq_align_dragmap_PE": { - "content": [ - "test.bam", - [ - "decompHashTableCtxInit...", - "decompHashTableHeader...", - "decompHashTableLiterals...", - "decompHashTableExtIndex...", - "decompHashTableAutoHits...", - "decompHashTableSetFlags..." - ] - ], - "timestamp": "2026-02-18T13:45:07.40135", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test_fastq_align_strobealign_PE": { "content": [ { - "0": [ + "bam": [ [ { "id": "test", "single_end": false }, - "test.bam:md5,1d8fb5dce75cbfb87955c7ee03c17a5f" + "test.bam:md5Reads,f3a1593b170cf1e9b9008b3afb77cc53" ] ], - "1": [ - - ], - "2": [ + "bam_index": [ ], + "reports": [ + [ + { + "id": "test", + "single_end": false + }, + "test.dragmap.log" + ] + ] + } + ], + "timestamp": "2026-08-25T15:16:50.038131", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "test_fastq_align_strobealign_PE": { + "content": [ + { "bam": [ [ { "id": "test", "single_end": false }, - "test.bam:md5,1d8fb5dce75cbfb87955c7ee03c17a5f" + "test.bam:md5Reads,f3a1593b170cf1e9b9008b3afb77cc53" ] ], "bam_index": [ @@ -68,164 +77,184 @@ ] } ], - "timestamp": "2026-02-18T14:49:56.04299", + "timestamp": "2026-08-25T14:47:40.847004", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "test_fastq_align_bwa_mem_SE": { "content": [ - "test.bam", - [ - - ], - [ - - ] + { + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5Reads,94fcf617f5b994584c4e8d4044e16b4f" + ] + ], + "bam_index": [ + + ], + "reports": [ + + ] + } ], - "timestamp": "2026-02-18T14:48:28.855536", + "timestamp": "2026-08-25T14:46:15.986784", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "test_fastq_align_bwamem2_SE": { "content": [ - "test.bam", - [ - - ], - [ - - ] + { + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5Reads,94fcf617f5b994584c4e8d4044e16b4f" + ] + ], + "bam_index": [ + + ], + "reports": [ + + ] + } ], - "timestamp": "2026-02-18T14:48:54.331973", + "timestamp": "2026-08-25T14:46:40.655059", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "test_fastq_align_bwa_mem_PE": { "content": [ - "test.bam", - [ - - ], - [ - - ] + { + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5Reads,af8628d9df18b2d3d4f6fd47ef2bb872" + ] + ], + "bam_index": [ + + ], + "reports": [ + + ] + } ], - "timestamp": "2026-02-18T14:48:37.392571", + "timestamp": "2026-08-25T14:46:23.735647", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "test_fastq_align_bowtie2_SE": { - "content": [ - "test.bam" - ], - "timestamp": "2026-02-18T14:48:09.863021", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test_fastq_align_dragmap_SE": { - "content": [ - "test.bam", - [ - "decompHashTableCtxInit...", - "decompHashTableHeader...", - "decompHashTableLiterals...", - "decompHashTableExtIndex...", - "decompHashTableAutoHits...", - "decompHashTableSetFlags..." - ] - ], - "timestamp": "2026-02-18T13:49:05.298349", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test_fastq_align_bowtie2_PE": { - "content": [ - "test.bam" - ], - "timestamp": "2026-02-18T14:48:20.207038", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test_fastq_align_snapaligner_PE": { "content": [ { - "0": [ + "bam": [ [ { "id": "test", - "single_end": false + "single_end": true }, - "test.bam:md5,504bcc1ac7f8d8e1e728276a4ce4f4d4" + "test.bam" ] ], - "1": [ + "bam_index": [ ], - "2": [ + "reports": [ - ], + ] + } + ], + "timestamp": "2026-08-25T15:55:57.09952", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "test_fastq_align_dragmap_SE": { + "content": [ + { "bam": [ [ { "id": "test", - "single_end": false + "single_end": true }, - "test.bam:md5,504bcc1ac7f8d8e1e728276a4ce4f4d4" + "test.bam:md5Reads,94fcf617f5b994584c4e8d4044e16b4f" ] ], "bam_index": [ ], "reports": [ - + [ + { + "id": "test", + "single_end": true + }, + "test.dragmap.log" + ] ] } ], - "timestamp": "2026-02-18T14:49:42.350796", + "timestamp": "2026-08-25T15:16:40.507415", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, - "test_fastq_align_strobealign_SE": { + "test_fastq_align_bowtie2_PE": { "content": [ { - "0": [ + "bam": [ [ { "id": "test", - "single_end": true + "single_end": false }, - "test.bam:md5,30a9339ac99b881844cf8514f719f204" + "test.bam" ] ], - "1": [ + "bam_index": [ ], - "2": [ + "reports": [ - ], + ] + } + ], + "timestamp": "2026-08-25T15:56:06.024816", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "test_fastq_align_snapaligner_PE": { + "content": [ + { "bam": [ [ { "id": "test", - "single_end": true + "single_end": false }, - "test.bam:md5,30a9339ac99b881844cf8514f719f204" + "test.bam:md5Reads,b16ca1648bc21cdec786100114477fb7" ] ], "bam_index": [ @@ -236,37 +265,48 @@ ] } ], - "timestamp": "2026-02-18T14:49:49.102483", + "timestamp": "2026-08-25T14:51:43.209925", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, - "test_fastq_align_snapaligner_SE": { + "test_fastq_align_strobealign_SE": { "content": [ { - "0": [ + "bam": [ [ { "id": "test", "single_end": true }, - "test.bam:md5,9de00a20df23dc66ddf0d9bba2e486c3" + "test.bam:md5Reads,94fcf617f5b994584c4e8d4044e16b4f" ] ], - "1": [ + "bam_index": [ ], - "2": [ + "reports": [ - ], + ] + } + ], + "timestamp": "2026-08-25T14:47:35.12633", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "test_fastq_align_snapaligner_SE": { + "content": [ + { "bam": [ [ { "id": "test", "single_end": true }, - "test.bam:md5,9de00a20df23dc66ddf0d9bba2e486c3" + "test.bam:md5Reads,798439cbd7fd81cbcc5078022dc5479d" ] ], "bam_index": [ @@ -277,10 +317,10 @@ ] } ], - "timestamp": "2026-02-18T14:49:34.584076", + "timestamp": "2026-08-25T14:47:23.556599", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml index e5c3a0a8..90430439 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -16,11 +16,11 @@ input: type: boolean description: | Dump the parameters of the pipeline to a JSON file - - output_directory: + - outdir: type: directory description: Path to output dir to write JSON file to. pattern: "results/" - - check_conda_channel: + - check_conda_channels: type: boolean description: | Check if the conda channel priority is correct. diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml index d08d2434..a32b454d 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -13,10 +13,10 @@ input: description: | Nextflow CLI positional arguments output: - - success: + - valid_config: type: boolean description: | - Dummy output to indicate success + Whether a custom configuration or profile was provided to the pipeline authors: - "@adamrtalbot" maintainers: diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 0d9d4e0d..340a5cc9 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -28,6 +28,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { if(help || help_full) { help_options = [ + parameter: (help instanceof String && help != "true") ? help : null, beforeText: before_text, afterText: after_text, command: command, @@ -35,12 +36,10 @@ workflow UTILS_NFSCHEMA_PLUGIN { fullHelp: help_full, ] if(parameters_schema) { - help_options << [parametersSchema: parameters_schema] + help_options << [parameters_schema: parameters_schema] } - log.info paramsHelp( - help_options, - (help instanceof String && help != "true") ? help : "", - ) + + log.info paramsHelp(help_options) exit 0 } @@ -51,10 +50,10 @@ workflow UTILS_NFSCHEMA_PLUGIN { summary_options = [:] if(parameters_schema) { - summary_options << [parametersSchema: parameters_schema] + summary_options << [parameters_schema: parameters_schema] } log.info before_text - log.info paramsSummaryLog(summary_options, input_workflow) + log.info paramsSummaryLog(summary_options) log.info after_text // @@ -64,10 +63,10 @@ workflow UTILS_NFSCHEMA_PLUGIN { if(validate_params) { validateOptions = [:] if(parameters_schema) { - validateOptions << [parametersSchema: parameters_schema] + validateOptions << [parameters_schema: parameters_schema] } if(cli_typecast != null) { - validateOptions << [cliTypecast: cli_typecast] + validateOptions << [cast_cli_params: cli_typecast] } validateParameters(validateOptions) } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index fd71cb8f..fcdb79c3 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.7.2" + id "nf-schema@3.0.0" } validation { diff --git a/tests/.nftignore b/tests/.nftignore index e128a128..fe9983ee 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,12 +1,6 @@ .DS_Store -multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt -multiqc/multiqc_data/multiqc.parquet -multiqc/multiqc_data/multiqc.log -multiqc/multiqc_data/multiqc_data.json -multiqc/multiqc_data/multiqc_sources.txt -multiqc/multiqc_data/multiqc_software_versions.txt -multiqc/multiqc_data/llms-full.txt -multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} -multiqc/multiqc_report.html -fastqc/*_fastqc.{html,zip} +multiqc/* +Reports/* +Logs/* +*/**/*.html pipeline_info/*.{html,json,txt,yml} diff --git a/tests/config/igenomes_test.config b/tests/config/igenomes_test.config index c3b2802d..1a9e79a2 100644 --- a/tests/config/igenomes_test.config +++ b/tests/config/igenomes_test.config @@ -1,11 +1,10 @@ -params.genomes = [ - GRCh38: [ - bwamem : "s3://test-data/genomics/homo_sapiens/genome/bwa/", - dict : "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - fai : "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - fasta : "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - star : "s3://test-data/genomics/homo_sapiens/genome/star/", - gtf : "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf", - genelists : "s3://test-data/genomics/homo_sapiens/genome/regions/genelists", - ] -] +params.genomes = [GRCh38: [ + bwamem: "s3://test-data/genomics/homo_sapiens/genome/bwa/", + snap: "s3://test-data/genomics/homo_sapiens/genome/snap/", + dict: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + fai: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + fasta: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + star: "s3://test-data/genomics/homo_sapiens/genome/star/", + gtf: "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf", + genelists: "s3://test-data/genomics/homo_sapiens/genome/regions/genelists", +]] diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config deleted file mode 100644 index 4bdc1c59..00000000 --- a/tests/config/nf-test.config +++ /dev/null @@ -1,11 +0,0 @@ -process { - resourceLimits = [ - cpus: 2, - memory: 6.GB, - time: 6.h, - ] -} - -params { - split_fastq = 100000000 -} diff --git a/tests/default.nf.test b/tests/default.nf.test index d32cc960..62f54b56 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -1,13 +1,12 @@ nextflow_pipeline { - name "Test Workflow main.nf" - script "main.nf" - config "tests/config/igenomes_test.config" + name "Test pipeline" + script "../main.nf" + config "./config/igenomes_test.config" tag "pipeline" - tag "pipeline/main" - test("main") { + test("-profile test") { when { params { @@ -18,9 +17,21 @@ nextflow_pipeline { } then { + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'multiqc', 'Reports', 'InterOp', 'Logs', '*/**/multiqc']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success + assertAll( + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/preprocessing_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content + ).match() } + ) } - } - } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 00000000..8d684617 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,420 @@ +{ + "-profile test": { + "content": [ + 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index 3a432b4b..ebc02d8f 100644 --- a/tests/inputs/test.yml +++ b/tests/inputs/test.yml @@ -13,7 +13,7 @@ tag: WES aligner: bwamem markdup: bamsormadup - run_coverage: true + qc_mode: basic fastq_1: https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/fastq/sample1_R1.fastq.gz fastq_2: https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/fastq/sample1_R2.fastq.gz - id: DNA1_L002 @@ -23,7 +23,7 @@ tag: WES aligner: bwamem markdup: bamsormadup - run_coverage: true + qc_mode: basic fastq_1: https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/test_R1.fastq.gz fastq_2: https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/test_R2.fastq.gz # RNA fastq inputs @@ -35,7 +35,7 @@ sample_type: RNA aligner: star markdup: bamsormadup - run_coverage: true + qc_mode: basic fastq_1: https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/fastq/sample1_R1.fastq.gz fastq_2: https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/fastq/sample1_R2.fastq.gz - id: RNA1_L002 @@ -46,6 +46,21 @@ sample_type: RNA aligner: star markdup: bamsormadup - run_coverage: true + qc_mode: basic fastq_1: https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/test_R1.fastq.gz fastq_2: https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/test_R2.fastq.gz +- id: umi_sample + samplename: umi_sample + library: test_library + organism: Homo sapiens + tag: WES + sample_type: DNA + aligner: snap + markdup: false + call_consensus: true + fgumi_extract_mode: read_structures + fgumi_read_structure_r1: 3M3S+T + fgumi_read_structure_r2: +T + qc_mode: basic + fastq_1: https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/sample1_S31_R1_001.fastq.gz + fastq_2: https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/illumina/fastq/sample1_S31_R2_001.fastq.gz diff --git a/tests/nextflow.config b/tests/nextflow.config index 548fbe63..70255513 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -1 +1,29 @@ -includeConfig "config/nf-test.config" +/* +======================================================================================== + Nextflow config file for running nf-test tests +======================================================================================== +*/ + +// TODO nf-core: Specify any additional parameters here +// Or any resources requirements +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/preprocessing/' +} + +includeConfig "../tests/config/igenomes_test.config" + +aws { + client { + endpoint = 'https://s3.ugent.be' + s3PathStyleAccess = true + } +} + +process { + resourceLimits = [ + cpus: 2, + memory: 6.GB, + time: 6.h, + ] +} diff --git a/tests/subworkflows/local/bam_qc/main.nf.test b/tests/subworkflows/local/bam_qc/main.nf.test deleted file mode 100644 index acb2f53a..00000000 --- a/tests/subworkflows/local/bam_qc/main.nf.test +++ /dev/null @@ -1,105 +0,0 @@ -nextflow_workflow { - - name "Test Workflow BAM_QC" - script "subworkflows/local/bam_qc/main.nf" - workflow "BAM_QC" - - tag "subworkflows" - tag "subworkflows/local" - tag "subworkflows/local/bam_qc" - - test("Bam QC - HSmetrics") { - - when { - workflow { - """ - // [meta, bam, bai, roi, fasta, fai, dict] - input[0] = Channel.of([ - [ id:'test', single_end:false, disable_picard_metrics:false ], - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists: true), - ]) - """ - } - } - - then { - assert workflow.success - assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "picard_wgsmetrics", - "picard_multiplemetrics_pdf", - "picard_multiplemetrics", - "picard_hsmetrics" - ]) - ).match() - } - - } - - test("Bam QC - WGSmetrics") { - when { - workflow { - """ - // [meta, bam, bai, roi, fasta, fai, dict] - input[0] = Channel.of([ - [ id:'test', single_end:false, disable_picard_metrics:false ], - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), - [], - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists: true), - ]) - """ - } - } - - then { - assert workflow.success - assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "picard_wgsmetrics", - "picard_multiplemetrics_pdf", - "picard_multiplemetrics", - "picard_hsmetrics" - ]) - ).match() - } - } - - test("Bam QC - Samtools") { - when { - workflow { - """ - // [meta, bam, bai, roi, fasta, fai, dict] - input[0] = Channel.of([ - [ id:'test', single_end:false, disable_picard_metrics:true ], - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", checkIfExists: true), - ]) - """ - } - } - - then { - assert workflow.success - assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "picard_wgsmetrics", - "picard_multiplemetrics_pdf", - "picard_multiplemetrics", - "picard_hsmetrics" - ]) - ).match() - } - } -} diff --git a/tests/subworkflows/local/bam_qc/main.nf.test.snap b/tests/subworkflows/local/bam_qc/main.nf.test.snap deleted file mode 100644 index 0f1dea8d..00000000 --- a/tests/subworkflows/local/bam_qc/main.nf.test.snap +++ /dev/null @@ -1,227 +0,0 @@ -{ - "Bam QC - HSmetrics": { - "content": [ - { - "picard_hsmetrics": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - "test.CollectHsMetrics.coverage_metrics" - ] - ], - "picard_multiplemetrics": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "picard_multiplemetrics_pdf": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ] - ] - ], - "picard_wgsmetrics": [ - - ], - "samtools_flagstat": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.flagstat:md5,167e69b479663a15194ddf56cbc9e60e" - ] - ], - "samtools_idxstats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.idxstats:md5,081d0431383fb7ea6b51b7077c6ec93c" - ] - ], - "samtools_stats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.stats:md5,ff81063faa5cf509f16044c4160733b5" - ] - ] - } - ], - "timestamp": "2026-03-25T18:43:20.761133", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - } - }, - "Bam QC - Samtools": { - "content": [ - { - "picard_hsmetrics": [ - - ], - "picard_multiplemetrics": [ - - ], - "picard_multiplemetrics_pdf": [ - - ], - "picard_wgsmetrics": [ - - ], - "samtools_flagstat": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": true - }, - "test.flagstat:md5,167e69b479663a15194ddf56cbc9e60e" - ] - ], - "samtools_idxstats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": true - }, - "test.idxstats:md5,081d0431383fb7ea6b51b7077c6ec93c" - ] - ], - "samtools_stats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": true - }, - "test.stats:md5,ff81063faa5cf509f16044c4160733b5" - ] - ] - } - ], - "timestamp": "2026-03-25T18:44:55.125939", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - } - }, - "Bam QC - WGSmetrics": { - "content": [ - { - "picard_hsmetrics": [ - - ], - "picard_multiplemetrics": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.alignment_summary_metrics", - "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "test.CollectMultipleMetrics.insert_size_metrics", - "test.CollectMultipleMetrics.quality_by_cycle_metrics", - "test.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "picard_multiplemetrics_pdf": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - [ - "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "test.CollectMultipleMetrics.insert_size_histogram.pdf", - "test.CollectMultipleMetrics.quality_by_cycle.pdf", - "test.CollectMultipleMetrics.quality_distribution.pdf", - "test.CollectMultipleMetrics.read_length_histogram.pdf" - ] - ] - ], - "picard_wgsmetrics": [ - [ - { - "disable_picard_metrics": false, - "id": "test", - "single_end": false - }, - "test.CollectWgsMetrics.coverage_metrics" - ] - ], - "samtools_flagstat": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.flagstat:md5,167e69b479663a15194ddf56cbc9e60e" - ] - ], - "samtools_idxstats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.idxstats:md5,081d0431383fb7ea6b51b7077c6ec93c" - ] - ], - "samtools_stats": [ - [ - { - "id": "test", - "single_end": false, - "disable_picard_metrics": false - }, - "test.stats:md5,ff81063faa5cf509f16044c4160733b5" - ] - ] - } - ], - "timestamp": "2026-03-25T18:44:25.625109", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file diff --git a/tests/subworkflows/local/coverage/main.nf.test b/tests/subworkflows/local/coverage/main.nf.test deleted file mode 100644 index c13bd512..00000000 --- a/tests/subworkflows/local/coverage/main.nf.test +++ /dev/null @@ -1,67 +0,0 @@ -nextflow_workflow { - - name "Test Workflow COVERAGE" - script "subworkflows/local/coverage/main.nf" - workflow "COVERAGE" - - tag "subworkflows" - tag "subworkflows/local" - tag "subworkflows/local/coverage" - - test("Coverage - seqcap") { - - when { - workflow { - """ - // ch_meta_cram_crai_fasta_fai_roi - input[0] = Channel.of([ - [id: "test", single_end: false, tag: "seqcap"], // meta - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), - ]) - // genelists - def genelists_path = "s3://test-data/genomics/homo_sapiens/genome/regions/genelists" - input[1] = channel.fromPath(genelists_path + "/*.bed").collect().map{ files -> [ files ] }.ifEmpty { channel.empty() } - """ - } - } - - then { - assert workflow.success - assert snapshot(workflow.out).match() - } - - } - - test("Coverage - WES") { - - when { - workflow { - """ - // ch_meta_cram_crai_fasta_fai_roi - input[0] = Channel.of([ - [id: "test", single_end: false, tag: "WES"], // meta - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/cram/sample1.sorted.cram.crai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", checkIfExists: true), - file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", checkIfExists: true), - ]) - // genelists - def genelists_path = "s3://test-data/genomics/homo_sapiens/genome/regions/genelists" - input[1] = channel.fromPath(genelists_path + "/*.bed").collect().map{ files -> [ files ] }.ifEmpty { channel.empty() } - """ - } - } - - then { - assert workflow.success - assert snapshot(workflow.out).match() - } - - } - -} diff --git a/tests/subworkflows/local/coverage/main.nf.test.snap b/tests/subworkflows/local/coverage/main.nf.test.snap deleted file mode 100644 index 0f1a2d18..00000000 --- a/tests/subworkflows/local/coverage/main.nf.test.snap +++ /dev/null @@ -1,506 +0,0 @@ -{ - "Coverage - WES": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.mosdepth.global.dist.txt:md5,ceec5e216dac6a4e15b961713ee8b16c" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.mosdepth.summary.txt:md5,c929389c608f49ca01d800fb5cc94bb9" - ] - ], - "10": [ - - ], - "11": [ - - ], - "12": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.coverage.txt:md5,2d81e108bf4175f2b892ab6e749fdf92" - ] - ], - "13": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - [ - "test_Treatable_ID_per_exon.mosdepth.region.dist.txt:md5,6c2b5237d98e0a2f118a3553c2ba478e", - "test_bladder_cancer_per_exon.mosdepth.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.mosdepth.region.dist.txt:md5,baffaa91e753347fd44c2e6e0a618d1f" - ] - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.per-base.bed.gz:md5,c89a207273626f8415df1710bc522e8e" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.per-base.bed.gz.csi:md5,c89ce701cf04e44aa49f54e2341c4bf0" - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.regions.bed.gz:md5,82848481047cda38748ec0409db8a669" - ] - ], - "7": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.regions.bed.gz.csi:md5,d128b1a1648ebc007d22b5c4a23663a6" - ] - ], - "8": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.quantized.bed.gz:md5,8975e3f5a62bb2ea6f349539daf8e9a4" - ] - ], - "9": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.quantized.bed.gz.csi:md5,a4dd4f2635eaa215cc92ec03d754e955" - ] - ], - "mosdepth_global": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.mosdepth.global.dist.txt:md5,ceec5e216dac6a4e15b961713ee8b16c" - ] - ], - "mosdepth_per_base_bed": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.per-base.bed.gz:md5,c89a207273626f8415df1710bc522e8e" - ] - ], - "mosdepth_per_base_csi": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.per-base.bed.gz.csi:md5,c89ce701cf04e44aa49f54e2341c4bf0" - ] - ], - "mosdepth_per_base_d4": [ - - ], - "mosdepth_quantized_bed": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.quantized.bed.gz:md5,8975e3f5a62bb2ea6f349539daf8e9a4" - ] - ], - "mosdepth_quantized_csi": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.quantized.bed.gz.csi:md5,a4dd4f2635eaa215cc92ec03d754e955" - ] - ], - "mosdepth_regions": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.mosdepth.region.dist.txt:md5,baffaa91e753347fd44c2e6e0a618d1f" - ] - ], - "mosdepth_regions_bed": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.regions.bed.gz:md5,82848481047cda38748ec0409db8a669" - ] - ], - "mosdepth_regions_csi": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.regions.bed.gz.csi:md5,d128b1a1648ebc007d22b5c4a23663a6" - ] - ], - "mosdepth_summary": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.mosdepth.summary.txt:md5,c929389c608f49ca01d800fb5cc94bb9" - ] - ], - "mosdepth_thresholds_bed": [ - - ], - "mosdepth_thresholds_csi": [ - - ], - "panelcoverage": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - [ - "test_Treatable_ID_per_exon.mosdepth.region.dist.txt:md5,6c2b5237d98e0a2f118a3553c2ba478e", - "test_bladder_cancer_per_exon.mosdepth.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "samtools_coverage": [ - [ - { - "id": "test", - "single_end": false, - "tag": "WES" - }, - "test.coverage.txt:md5,2d81e108bf4175f2b892ab6e749fdf92" - ] - ] - } - ], - "timestamp": "2026-04-30T14:26:13.856281842", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, - "Coverage - seqcap": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.mosdepth.global.dist.txt:md5,ceec5e216dac6a4e15b961713ee8b16c" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.mosdepth.summary.txt:md5,c929389c608f49ca01d800fb5cc94bb9" - ] - ], - "10": [ - - ], - "11": [ - - ], - "12": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.coverage.txt:md5,2d81e108bf4175f2b892ab6e749fdf92" - ] - ], - "13": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test_seqcap_Connective_tissue_per_exon.mosdepth.region.dist.txt:md5,e098c901acb1da8c2cf64a248306e71c" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.mosdepth.region.dist.txt:md5,baffaa91e753347fd44c2e6e0a618d1f" - ] - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.per-base.bed.gz:md5,c89a207273626f8415df1710bc522e8e" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.per-base.bed.gz.csi:md5,c89ce701cf04e44aa49f54e2341c4bf0" - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.regions.bed.gz:md5,82848481047cda38748ec0409db8a669" - ] - ], - "7": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.regions.bed.gz.csi:md5,d128b1a1648ebc007d22b5c4a23663a6" - ] - ], - "8": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.quantized.bed.gz:md5,8975e3f5a62bb2ea6f349539daf8e9a4" - ] - ], - "9": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.quantized.bed.gz.csi:md5,a4dd4f2635eaa215cc92ec03d754e955" - ] - ], - "mosdepth_global": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.mosdepth.global.dist.txt:md5,ceec5e216dac6a4e15b961713ee8b16c" - ] - ], - "mosdepth_per_base_bed": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.per-base.bed.gz:md5,c89a207273626f8415df1710bc522e8e" - ] - ], - "mosdepth_per_base_csi": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.per-base.bed.gz.csi:md5,c89ce701cf04e44aa49f54e2341c4bf0" - ] - ], - "mosdepth_per_base_d4": [ - - ], - "mosdepth_quantized_bed": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.quantized.bed.gz:md5,8975e3f5a62bb2ea6f349539daf8e9a4" - ] - ], - "mosdepth_quantized_csi": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.quantized.bed.gz.csi:md5,a4dd4f2635eaa215cc92ec03d754e955" - ] - ], - "mosdepth_regions": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.mosdepth.region.dist.txt:md5,baffaa91e753347fd44c2e6e0a618d1f" - ] - ], - "mosdepth_regions_bed": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.regions.bed.gz:md5,82848481047cda38748ec0409db8a669" - ] - ], - "mosdepth_regions_csi": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.regions.bed.gz.csi:md5,d128b1a1648ebc007d22b5c4a23663a6" - ] - ], - "mosdepth_summary": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.mosdepth.summary.txt:md5,c929389c608f49ca01d800fb5cc94bb9" - ] - ], - "mosdepth_thresholds_bed": [ - - ], - "mosdepth_thresholds_csi": [ - - ], - "panelcoverage": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test_seqcap_Connective_tissue_per_exon.mosdepth.region.dist.txt:md5,e098c901acb1da8c2cf64a248306e71c" - ] - ], - "samtools_coverage": [ - [ - { - "id": "test", - "single_end": false, - "tag": "seqcap" - }, - "test.coverage.txt:md5,2d81e108bf4175f2b892ab6e749fdf92" - ] - ] - } - ], - "timestamp": "2026-04-30T14:25:39.573281873", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file diff --git a/tests/workflows/preprocessing.nf.test b/tests/workflows/preprocessing.nf.test index c2770b1a..1494f785 100644 --- a/tests/workflows/preprocessing.nf.test +++ b/tests/workflows/preprocessing.nf.test @@ -7,7 +7,7 @@ nextflow_workflow { tag "workflows" tag "workflows/preprocessing" - test("preprocessing - fastq - bwa - bamsormadup - roi") { + test("preprocessing - fastq - bwa - bamsormadup - roi - full qc") { when { workflow { @@ -24,7 +24,7 @@ nextflow_workflow { sample_type: "DNA", aligner: "bwamem", markdup: "bamsormadup", - run_coverage: true, + qc_mode: "full", roi: "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed" ], //fastq_1 @@ -63,32 +63,31 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "crams", - "fastp_html", - "md5sums", - "mosdepth_per_base_csi", - "mosdepth_quantized_csi", - "mosdepth_regions_csi", - "multiqc_data", - "multiqc_plots", - "multiqc_report", - "multiqcsav_data", - "multiqcsav_plots", - "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", - "samtools_coverage", - "samtools_flagstat", - "samtools_stats" - ]) + sanitizeOutput( + workflow.out, + unstableKeys:[ + "crams", + "fastp_html", + "md5sums", + "mosdepth_per_base_csi", + "mosdepth_quantized_csi", + "mosdepth_regions_csi", + "multiqc_data", + "multiqc_plots", + "multiqc_report", + "multiqcsav_data", + "multiqcsav_plots", + "multiqcsav_report", + "riker_hybcap_metrics", + "riker_isize_histogram", + "riker_pdf" + ] + ) ).match() } } - test("preprocessing - fastq - bwa - bamsormadup - no roi") { + test("preprocessing - fastq - bwa - bamsormadup - no roi - full qc") { when { workflow { @@ -105,7 +104,7 @@ nextflow_workflow { sample_type: "DNA", aligner: "bwamem", markdup: "bamsormadup", - run_coverage: true + qc_mode: "full" ], //fastq_1 file("https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/fastq/sample1_R1.fastq.gz", checkIfExists: true), @@ -144,36 +143,33 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "crams", - "fastp_html", - "md5sums", - "mosdepth_per_base_csi", - "mosdepth_quantized_csi", - "mosdepth_regions_csi", - "multiqc_data", - "multiqc_plots", - "multiqc_report", - "multiqcsav_data", - "multiqcsav_plots", - "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", - "samtools_coverage", - "samtools_flagstat", - "samtools_stats" - ]) + sanitizeOutput( + workflow.out, + unstableKeys:[ + "crams", + "fastp_html", + "md5sums", + "mosdepth_per_base_csi", + "mosdepth_quantized_csi", + "mosdepth_regions_csi", + "multiqc_data", + "multiqc_plots", + "multiqc_report", + "multiqcsav_data", + "multiqcsav_plots", + "multiqcsav_report", + "riker_hybcap_metrics", + "riker_isize_histogram", + "riker_pdf" + ] + ) ).match() } } - test("preprocessing - fastq - bwa - bamsormadup - roi - no coverage/no picard") { + test("preprocessing - fastq - bwa - bamsormadup - roi - basic qc") { when { params { - run_coverage = false - disable_picard_metrics = true } workflow { """ @@ -189,8 +185,7 @@ nextflow_workflow { sample_type: "DNA", aligner: "bwamem", markdup: "bamsormadup", - run_coverage: false, - disable_picard_metrics: true, + qc_mode: "basic", roi: "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed" ], //fastq_1 @@ -230,32 +225,31 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "crams", - "fastp_html", - "md5sums", - "mosdepth_per_base_csi", - "mosdepth_quantized_csi", - "mosdepth_regions_csi", - "multiqc_data", - "multiqc_plots", - "multiqc_report", - "multiqcsav_data", - "multiqcsav_plots", - "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", - "samtools_coverage", - "samtools_flagstat", - "samtools_stats" - ]) + sanitizeOutput( + workflow.out, + unstableKeys:[ + "crams", + "fastp_html", + "md5sums", + "mosdepth_per_base_csi", + "mosdepth_quantized_csi", + "mosdepth_regions_csi", + "multiqc_data", + "multiqc_plots", + "multiqc_report", + "multiqcsav_data", + "multiqcsav_plots", + "multiqcsav_report", + "riker_hybcap_metrics", + "riker_isize_histogram", + "riker_pdf" + ] + ) ).match() } } - test("preprocessing - flowcell - bwa - bamsormadup - roi") { + test("preprocessing - flowcell - bwa - bamsormadup - roi - basic qc") { when { workflow { """ @@ -301,37 +295,29 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - sanitizeOutput(workflow.out, unstableKeys:[ - "crams", - "demultiplex_logs", - "demultiplex_reports", - "fastp_html", - "md5sums", - "mosdepth_per_base_csi", - "mosdepth_quantized_csi", - "mosdepth_regions_csi", - "multiqc_data", - "multiqc_plots", - "multiqc_report", - "multiqcsav_data", - "multiqcsav_plots", - "multiqcsav_report", - "picard_hsmetrics", - "picard_multiplemetrics", - "picard_multiplemetrics_pdf", - "picard_wgsmetrics", - "samtools_coverage", - "samtools_flagstat", - "samtools_stats" - ]).collectEntries { key, value -> - if (key in ["demultiplex_logs", "demultiplex_reports"]) { - [ key: value.sort() ] - } else { - [ key: value ] - } - } + sanitizeOutput( + workflow.out, + unstableKeys:[ + "crams", + "falco_html", + "fastp_html", + "md5sums", + "mosdepth_per_base_csi", + "mosdepth_quantized_csi", + "mosdepth_regions_csi", + "multiqc_data", + "multiqc_plots", + "multiqc_report", + "multiqcsav_data", + "multiqcsav_plots", + "multiqcsav_report", + "riker_hybcap_metrics", + "riker_isize_histogram", + "riker_pdf", + ], + ignoreKeys: ["demultiplex_logs", "demultiplex_reports"] + ) ).match() } } - } diff --git a/tests/workflows/preprocessing.nf.test.snap b/tests/workflows/preprocessing.nf.test.snap index 5338b7c2..40e26512 100644 --- a/tests/workflows/preprocessing.nf.test.snap +++ b/tests/workflows/preprocessing.nf.test.snap @@ -1,5 +1,5 @@ { - "preprocessing - fastq - bwa - bamsormadup - roi": { + "preprocessing - fastq - bwa - bamsormadup - no roi - full qc": { "content": [ { "align_reports": [ @@ -23,12 +23,11 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, "sample1.cram", @@ -67,20 +66,18 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", + "qc_mode": "full", "readgroup": { - "CN": "", "ID": "H5T2YDSX3.1", "LB": "test", "PL": "ILLUMINA", "PU": "H5T2YDSX3.1", "SM": "sample1" }, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" }, "sample1.fastp.html" ] @@ -88,36 +85,34 @@ "fastp_json": [ [ { + "aligner": "bwamem", + "count": 1, + "genome": "GRCh38", + "genome_data": { + "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", + "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" + }, "id": "sample1", - "samplename": "sample1", "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", - "aligner": "bwamem", "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, + "organism": "Homo sapiens", + "qc_mode": "full", "readgroup": { + "ID": "H5T2YDSX3.1", "LB": "test", - "CN": "", "PL": "ILLUMINA", - "SM": "sample1", - "ID": "H5T2YDSX3.1", - "PU": "H5T2YDSX3.1" - }, - "genome": "GRCh38", - "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" + "PU": "H5T2YDSX3.1", + "SM": "sample1" }, - "count": 1 + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WGS" }, - "sample1.fastp.json:md5,759cb3337e9a02f54a9dcb7582288a60" + "sample1.fastp.json:md5,ed04a7b4cbf74e7b5f4594227a406ffa" ] ], "fastq": [ @@ -141,12 +136,11 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, "sample1.md5" @@ -157,28 +151,27 @@ { "groupSize": 1, "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, "genome": "GRCh38", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" }, - "id": "sample1" + "id": "sample1", + "library": "test", + "markdup": "bamsormadup", + "organism": "Homo sapiens", + "qc_mode": "full", + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WGS" } }, - "sample1.mosdepth.global.dist.txt:md5,4574a0f755903d7ab7aa07297cc1efee" + "sample1.mosdepth.global.dist.txt:md5,c040c96ab1744361a7d18129aa24ec17" ] ], "mosdepth_per_base_bed": [ @@ -186,28 +179,27 @@ { "groupSize": 1, "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, "genome": "GRCh38", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" }, - "id": "sample1" + "id": "sample1", + "library": "test", + "markdup": "bamsormadup", + "organism": "Homo sapiens", + "qc_mode": "full", + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WGS" } }, - "sample1.per-base.bed.gz:md5,e5c10c94f3870f6ed2c75a904e9ade7f" + "sample1.per-base.bed.gz:md5,a717c3ae016a09682a3cb42953626abd" ] ], "mosdepth_per_base_csi": [ @@ -228,12 +220,11 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, "sample1.per-base.bed.gz.csi" @@ -247,28 +238,27 @@ { "groupSize": 1, "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, "genome": "GRCh38", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", + "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", + "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", + "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" }, - "id": "sample1" + "id": "sample1", + "library": "test", + "markdup": "bamsormadup", + "organism": "Homo sapiens", + "qc_mode": "full", + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WGS" } }, - "sample1.quantized.bed.gz:md5,d54d469a692c3fe4a4e1db02c08be518" + "sample1.quantized.bed.gz:md5,e877ffaa3fb270adef307fb492477749" ] ], "mosdepth_quantized_csi": [ @@ -289,76 +279,26 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, "sample1.quantized.bed.gz.csi" ] ], "mosdepth_regions": [ - [ - { - "groupSize": 1, - "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", - "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, - "genome": "GRCh38", - "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1" - } - }, - "sample1.mosdepth.region.dist.txt:md5,388e05b0b4d7754be6fdc0b1b6eabed9" - ] + ], "mosdepth_regions_bed": [ - [ - { - "groupSize": 1, - "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", - "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, - "genome": "GRCh38", - "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1" - } - }, - "sample1.regions.bed.gz:md5,6b7cc84380695011ffd0681dc79cefaa" - ] + ], "mosdepth_regions_csi": [ + + ], + "mosdepth_summary": [ [ { "groupSize": 1, @@ -376,44 +316,14 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" - } - }, - "sample1.regions.bed.gz.csi" - ] - ], - "mosdepth_summary": [ - [ - { - "groupSize": 1, - "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", - "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, - "genome": "GRCh38", - "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "sample1" + "tag": "WGS" } }, - "sample1.mosdepth.summary.txt:md5,f1f18d9bd23783bedb7f9e246e192a7e" + "sample1.mosdepth.summary.txt:md5,e7b820f11ab98ae3e3c44c7422d0f7f6" ] ], "mosdepth_thresholds_bed": [ @@ -427,7 +337,80 @@ { "id": "test" }, - "test_data" + [ + "biobambam2_deduplication.txt", + "fastp-insert-size-plot.txt", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", + "fastp-seq-content-gc-plot_Read_2_After_filtering.txt", + "fastp-seq-content-gc-plot_Read_2_Before_filtering.txt", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt", + "fastp-seq-content-n-plot_Read_2_After_filtering.txt", + "fastp-seq-content-n-plot_Read_2_Before_filtering.txt", + "fastp-seq-quality-plot_Read_1_After_filtering.txt", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt", + "fastp-seq-quality-plot_Read_2_After_filtering.txt", + "fastp-seq-quality-plot_Read_2_Before_filtering.txt", + "fastp_filtered_reads_plot.txt", + "llms-full.txt", + "mosdepth-coverage-per-contig-single.txt", + "mosdepth-cumcoverage-dist-id.txt", + "mosdepth_cov_dist.txt", + "mosdepth_cumcov_dist.txt", + "mosdepth_perchrom.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_biobambam2_dups.txt", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastp.txt", + "multiqc_general_stats.txt", + "multiqc_riker_alignment.txt", + "multiqc_riker_basic_base_distribution.txt", + "multiqc_riker_basic_mean_quality_by_cycle.txt", + "multiqc_riker_basic_quality_score_distribution.txt", + "multiqc_riker_gcbias_detail.txt", + "multiqc_riker_gcbias_summary.txt", + "multiqc_riker_isize.txt", + "multiqc_riker_wgs.txt", + "multiqc_samtools_coverage.txt", + "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", + "multiqc_samtools_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt", + "riker_alignment_summary.txt", + "riker_alignment_table.txt", + "riker_base_distribution_by_cycle__A.txt", + "riker_base_distribution_by_cycle__C.txt", + "riker_base_distribution_by_cycle__G.txt", + "riker_base_distribution_by_cycle__N.txt", + "riker_base_distribution_by_cycle__T.txt", + "riker_gcbias_normalized_coverage.txt", + "riker_insert_size_FR.txt", + "riker_insert_size_RF.txt", + "riker_mean_quality_by_cycle.txt", + "riker_quality_score_distribution.txt", + "riker_wgs_coverage_histogram.txt", + "riker_wgs_excluded_bases.txt", + "riker_wgs_table.txt", + "samtools-coverage-table.txt", + "samtools-coverage_BQ.txt", + "samtools-coverage_Bases.txt", + "samtools-coverage_Coverage.txt", + "samtools-coverage_MQ.txt", + "samtools-coverage_Mean_depth.txt", + "samtools-coverage_Reads.txt", + "samtools-flagstat-pct-table.txt", + "samtools-flagstat-table.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", + "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", + "samtools_insert_size.txt" + ] ] ], "multiqc_plots": [ @@ -459,7 +442,7 @@ "panelcoverage": [ ], - "picard_hsmetrics": [ + "riker_alignment_metrics": [ [ { "groupSize": 1, @@ -477,18 +460,17 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, - "sample1.CollectHsMetrics.coverage_metrics" + "sample1.alignment-metrics.txt:md5,b7e1d8433e1e3ac164ae0df11d0e715c" ] ], - "picard_multiplemetrics": [ + "riker_base_dist": [ [ { "groupSize": 1, @@ -506,23 +488,26 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, - [ - "sample1.CollectMultipleMetrics.alignment_summary_metrics", - "sample1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "sample1.CollectMultipleMetrics.quality_by_cycle_metrics", - "sample1.CollectMultipleMetrics.quality_distribution_metrics" - ] + "sample1.base-distribution-by-cycle.txt:md5,7da0182f73031d3a29becfba74cf5a8c" ] ], - "picard_multiplemetrics_pdf": [ + "riker_error_indel": [ + + ], + "riker_error_mismatch": [ + + ], + "riker_error_overlap": [ + + ], + "riker_gcbias_detail": [ [ { "groupSize": 1, @@ -540,32 +525,17 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, - [ - "sample1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "sample1.CollectMultipleMetrics.quality_by_cycle.pdf", - "sample1.CollectMultipleMetrics.quality_distribution.pdf", - "sample1.CollectMultipleMetrics.read_length_histogram.pdf" - ] + "sample1.gcbias-detail.txt:md5,6e32c262bf2c35aa0619b89df3b19c3f" ] ], - "picard_wgsmetrics": [ - - ], - "rna_junctions": [ - - ], - "rna_splice_junctions": [ - - ], - "samtools_coverage": [ + "riker_gcbias_summary": [ [ { "groupSize": 1, @@ -583,18 +553,26 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, - "sample1.coverage.txt" + "sample1.gcbias-summary.txt:md5,ca3d89d83a8abd07720f84f68474b597" ] ], - "samtools_flagstat": [ + "riker_hybcap_metrics": [ + + ], + "riker_hybcap_per_base": [ + + ], + "riker_hybcap_per_target": [ + + ], + "riker_isize_histogram": [ [ { "groupSize": 1, @@ -612,47 +590,2173 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "run_coverage": true, + "qc_mode": "full", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WES" + "tag": "WGS" } }, - "sample1.flagstat" + "sample1.isize-histogram.txt" ] ], - "samtools_idxstats": [ + "riker_isize_metrics": [ [ { "groupSize": 1, "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WES", - "sample_type": "DNA", "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", - "single_end": false, "genome": "GRCh38", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": 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"https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WES" + } }, - "test.html" - ] - ], - "multiqcsav_data": [ - [ - - ] - ], - "multiqcsav_plots": [ - [ - - ] - ], - "multiqcsav_report": [ - [ - + "sample1.isize-metrics.txt:md5,ba8b257116ab05b3c365eb25804641e2" ] ], - "panelcoverage": [ - - ], - "picard_hsmetrics": [ - - ], - "picard_multiplemetrics": [ + "riker_mean_qual": [ [ { "groupSize": 1, @@ -1490,22 +3591,18 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "run_coverage": true, + "qc_mode": "full", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WGS" + "tag": "WES" } }, - [ - "sample1.CollectMultipleMetrics.alignment_summary_metrics", - 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-1590,14 +3708,15 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "run_coverage": true, + "qc_mode": "full", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WGS" + "tag": "WES" } }, - "sample1.coverage.txt" + "sample1.coverage.txt:md5,f9c7a6396f17209b2038c2d6ca77c1e9" ] ], "samtools_flagstat": [ @@ -1618,14 +3737,15 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "run_coverage": true, + "qc_mode": "full", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WGS" + "tag": "WES" } }, - "sample1.flagstat" + "sample1.flagstat:md5,e4e08d3241e03f6e7d7251efd4907e87" ] ], "samtools_idxstats": [ @@ -1633,27 +3753,28 @@ { 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"s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" }, - "id": "sample1" + "id": "sample1", + "library": "test", + "markdup": "bamsormadup", + "organism": "Homo sapiens", + "qc_mode": "full", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WES" } }, - "sample1.idxstats:md5,ecc89a474dced28b0610f17a82785007" + "sample1.idxstats:md5,a861f699339736abb64e36c17a9542f6" ] ], "samtools_stats": [ @@ -1674,14 +3795,15 @@ "library": "test", "markdup": "bamsormadup", "organism": "Homo sapiens", - "run_coverage": true, + "qc_mode": "full", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", "sample_type": "DNA", "samplename": "sample1", "single_end": false, - "tag": "WGS" + "tag": "WES" } }, - "sample1.stats" + "sample1.stats:md5,2969ffda928b816d2fd4690521f9c148" ] ], "sormadup_metrics": [ @@ -1689,94 +3811,36 @@ { "groupSize": 1, "groupTarget": { - "samplename": "sample1", - "library": "test", - "organism": "Homo sapiens", - "tag": "WGS", - "sample_type": "DNA", "aligner": "bwamem", - "markdup": "bamsormadup", - "run_coverage": true, - "single_end": false, "genome": "GRCh38", "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": 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{ - "groupSize": 1, - "groupTarget": { - "single_end": true, - "samplename": "Sample1", - "sample_type": "DNA", + "id": "sample1", "library": "test", - "tag": "WES", - "purpose": [ - - ], - "organism": "Homo sapiens", - "genome": "GRCh38", - "vivar_project": [ - - ], - "binsize": [ - - ], - "panels": [ - - ], - "aligner": "bwamem", "markdup": "bamsormadup", - "umi_aware": false, - "skip_trimming": false, - "trim_front": 0, - "trim_tail": 0, - "adapter_R1": null, - "adapter_R2": null, - "run_coverage": true, - "disable_picard_metrics": true, - "roi": null, - "genome_data": { - "fasta": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna", - "fai": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai", - "dict": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict", - "bwamem": "s3://test-data/genomics/homo_sapiens/genome/bwa/", - "gtf": "s3://test-data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.gtf" - }, - "id": "Sample1" + "organism": "Homo sapiens", + "qc_mode": "full", + "roi": "https://github.com/nf-cmgg/test-datasets/raw/preprocessing/data/genomics/homo_sapiens/illumina/regions/roi_chr21.bed", + "sample_type": "DNA", + "samplename": "sample1", + "single_end": false, + "tag": "WES" } }, - "Sample1.merged.metrics.txt:md5,f23933cc5957694d2286bdae22039097" + "sample1.merged.metrics.txt:md5,4d15baa69fa5af4d51cc9e2e4e3ecd35" ] ] } ], - "timestamp": "2026-05-19T12:26:24.789934", + "timestamp": "2026-09-09T14:55:56.636493", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/tower.yml b/tower.yml deleted file mode 100644 index 787aedfe..00000000 --- a/tower.yml +++ /dev/null @@ -1,5 +0,0 @@ -reports: - multiqc_report.html: - display: "MultiQC HTML report" - samplesheet.csv: - display: "Auto-created samplesheet with collated metadata and FASTQ paths" diff --git a/workflows/preprocessing.nf b/workflows/preprocessing.nf index 46c93597..921c3b64 100644 --- a/workflows/preprocessing.nf +++ b/workflows/preprocessing.nf @@ -17,12 +17,10 @@ include { SAMTOOLS_COVERAGE } from '../modules/nf-core/samtools/covera // Subworkflows include { BAM_QC } from '../subworkflows/local/bam_qc' -include { COVERAGE } from '../subworkflows/local/coverage' include { FASTQ_TO_CRAM } from '../subworkflows/local/fastq_to_aligned_cram' // Functions -include { getReadgroupsFromBclconvert } from '../subworkflows/local/utils_nfcmgg_preprocessing_pipeline' -include { getReadgroupFromFastq } from '../subworkflows/local/utils_nfcmgg_preprocessing_pipeline' +include { associateSampleinfo ; getReadgroupsFromBclconvert ; getReadgroupFromFastq } from '../subworkflows/local/utils_nfcmgg_preprocessing_pipeline' include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' @@ -83,7 +81,7 @@ workflow PREPROCESSING { return [meta, file(reports).resolve("fastq_list.csv")] }, BCLCONVERT.out.fastq, - ).dump(tag: "DEMULTIPLEX: fastq with meta", pretty: true).map { meta, fastq -> [meta.readgroup.SM, meta, fastq] }.set { ch_demultiplexed_fastq } + ).dump(tag: "DEMULTIPLEX: fastq with meta", pretty: true).set { ch_demultiplexed_fastq } // Run QC ch_mqcsav_input = ch_illumina_flowcell.flowcell @@ -110,12 +108,10 @@ workflow PREPROCESSING { ch_illumina_flowcell.info .flatten() .transpose() - .map { sampleinfo -> [sampleinfo.samplename, sampleinfo] } .set { ch_sampleinfo } - ch_demultiplexed_fastq - .combine(ch_sampleinfo, by: 0) - .map { _samplename, meta, fastq, sampleinfo -> + associateSampleinfo(ch_demultiplexed_fastq, ch_sampleinfo) + .map { meta, fastq, sampleinfo -> def new_rg = [:] if (sampleinfo.library) { new_rg = meta.readgroup + ['LB': sampleinfo.library] @@ -149,7 +145,7 @@ workflow PREPROCESSING { // add readgroup metadata // if the sample name starts with "snp_", remove it so the sampletracking works later on. def samplename = meta.samplename.startsWith("snp_") ? meta.samplename.substring(4) : meta.samplename - def rg = getReadgroupFromFastq(fastq[0], samplename, meta.library, meta.platform) + def rg = getReadgroupFromFastq(fastq[0], samplename, meta.library, meta.sequencing_center) def meta_with_readgroup = meta + ['single_end': single_end, 'readgroup': rg] return [meta_with_readgroup, fastq] } @@ -173,6 +169,9 @@ workflow PREPROCESSING { else if (meta.organism ==~ /(?i)Danio[\s_]rerio/) { meta = meta + ["genome": "GRCz11"] } + else if (meta.organism ==~ /(?i)Equus[\s_]caballus/) { + meta = meta + ["genome": "EquCab2"] + } else { meta = meta + ["genome": null] } @@ -185,7 +184,7 @@ workflow PREPROCESSING { } return [meta, reads] } - .map { meta, reads -> [meta.samplename, [meta, reads]] } + .map { meta, reads -> [[meta.samplename, meta.library], [meta, reads]] } .groupTuple() .map { _samplename, meta_fastq -> [meta_fastq, meta_fastq.size()] } .transpose() @@ -194,7 +193,7 @@ workflow PREPROCESSING { return [meta - meta.subMap('fcid', 'lane'), fastq] } .branch { meta, _reads -> - supported: meta.genome_data instanceof Map && meta.genome_data.size() > 0 && (meta.aligner && meta.aligner != "false") + supported: meta.genome_data instanceof Map && meta.genome_data.size() > 0 && meta.aligner other: true } .set { ch_fastq_per_sample } @@ -231,7 +230,7 @@ workflow PREPROCESSING { // edit meta.id to match sample name FASTP.out.reads .map { meta, reads -> - def read_files = meta.single_end.toBoolean() ? reads : reads.sort { a, b -> a.getName().tokenize('.')[0] <=> b.getName().tokenize('.')[0] }.collate(2) + def read_files = meta.single_end.toBoolean() ? reads : reads.sort { fq -> fq.name }.collate(2) return [ meta + [chunks: read_files instanceof List ? read_files.size() : [read_files].size()], read_files, @@ -271,35 +270,9 @@ workflow PREPROCESSING { FASTQ_TO_CRAM( ch_meta_reads_aligner_index_fasta_gtf ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TO_CRAM.out.sormadup_metrics) - - /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -// STEP: COVERAGE ANALYSIS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - FASTQ_TO_CRAM.out.cram_crai - .filter { meta, _cram, _crai -> - meta.run_coverage.toBoolean() - } - .map { meta, cram, crai -> - return [ - meta, - cram, - crai, - getGenomeAttribute(meta.genome_data, "fasta"), - getGenomeAttribute(meta.genome_data, "fai"), - meta.roi && meta.roi != [] ? file(meta.roi, checkIfExists: true) : [], - ] - } - .set { ch_coverage } - - COVERAGE(ch_coverage, ch_genelists) ch_multiqc_files = ch_multiqc_files.mix( - COVERAGE.out.mosdepth_summary, - COVERAGE.out.mosdepth_global, - COVERAGE.out.mosdepth_regions, - COVERAGE.out.samtools_coverage, + FASTQ_TO_CRAM.out.sormadup_metrics, + FASTQ_TO_CRAM.out.family_size_histogram, ) /* @@ -316,20 +289,36 @@ workflow PREPROCESSING { meta.roi && meta.roi != [] ? file(meta.roi, checkIfExists: true) : [], getGenomeAttribute(meta.genome_data, "fasta"), getGenomeAttribute(meta.genome_data, "fai"), - getGenomeAttribute(meta.genome_data, "dict"), + getGenomeAttribute(meta.genome_data, "gtf"), ] } .set { ch_bam_qc } - BAM_QC(ch_bam_qc) + BAM_QC(ch_bam_qc, ch_genelists) ch_multiqc_files = ch_multiqc_files.mix( - BAM_QC.out.samtools_stats, + BAM_QC.out.mosdepth_global, + BAM_QC.out.mosdepth_regions, + BAM_QC.out.mosdepth_summary, + BAM_QC.out.samtools_coverage, BAM_QC.out.samtools_flagstat, BAM_QC.out.samtools_idxstats, - BAM_QC.out.picard_multiplemetrics, - BAM_QC.out.picard_wgsmetrics, - BAM_QC.out.picard_wgsmetrics, - BAM_QC.out.picard_hsmetrics, + BAM_QC.out.samtools_stats, + BAM_QC.out.riker_alignment_metrics, + BAM_QC.out.riker_base_dist, + BAM_QC.out.riker_mean_qual, + BAM_QC.out.riker_qual_dist, + BAM_QC.out.riker_error_mismatch, + BAM_QC.out.riker_error_overlap, + BAM_QC.out.riker_error_indel, + BAM_QC.out.riker_gcbias_detail, + BAM_QC.out.riker_gcbias_summary, + BAM_QC.out.riker_hybcap_metrics, + BAM_QC.out.riker_hybcap_per_target, + BAM_QC.out.riker_hybcap_per_base, + BAM_QC.out.riker_isize_metrics, + BAM_QC.out.riker_isize_histogram, + BAM_QC.out.riker_wgs_metrics, + BAM_QC.out.riker_wgs_coverage, ) /* @@ -375,7 +364,7 @@ workflow PREPROCESSING { softwareVersionsToYAML(topic_versions.versions_file) .mix(topic_versions_string) .collectFile( - storeDir: "${outdir.toUriString()}/pipeline_info", + storeDir: "${outdir}/pipeline_info", name: 'nf_cmgg_preprocessing_software_mqc_versions.yml', sort: true, newLine: true, @@ -386,7 +375,7 @@ workflow PREPROCESSING { // MODULE: MultiQC // // summary files without meta, e.g. versions, params - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + summary_params = paramsSummaryMap(parameters_schema: "nextflow_schema.json") ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) ch_methods_description = channel.value(multiqc_methods_description ? methodsDescriptionText(multiqc_methods_description) : "") @@ -415,49 +404,66 @@ workflow PREPROCESSING { MULTIQC(ch_multiqc_input) emit: - demultiplex_reports = BCLCONVERT.out.reports.map { meta, reports -> + demultiplex_reports = BCLCONVERT.out.reports.map { meta, reports -> return [meta, files(reports.resolve("*"))] } - demultiplex_logs = BCLCONVERT.out.logs.map { meta, logs -> + demultiplex_logs = BCLCONVERT.out.logs.map { meta, logs -> return [meta, files(logs.resolve("*"))] } - demultiplex_interop = BCLCONVERT.out.interop - fastq = ch_fastq_per_sample.other - falco_html = FALCO.out.html - falco_txt = FALCO.out.txt - fastp_json = FASTP.out.json - fastp_html = FASTP.out.html - crams = FASTQ_TO_CRAM.out.cram_crai - rna_splice_junctions = FASTQ_TO_CRAM.out.rna_splice_junctions - rna_junctions = FASTQ_TO_CRAM.out.rna_junctions - align_reports = FASTQ_TO_CRAM.out.align_reports - sormadup_metrics = FASTQ_TO_CRAM.out.sormadup_metrics - mosdepth_global = COVERAGE.out.mosdepth_global - mosdepth_summary = COVERAGE.out.mosdepth_summary - mosdepth_regions = COVERAGE.out.mosdepth_regions - mosdepth_per_base_d4 = COVERAGE.out.mosdepth_per_base_d4 - mosdepth_per_base_bed = COVERAGE.out.mosdepth_per_base_bed - mosdepth_per_base_csi = COVERAGE.out.mosdepth_per_base_csi - mosdepth_regions_bed = COVERAGE.out.mosdepth_regions_bed - mosdepth_regions_csi = COVERAGE.out.mosdepth_regions_csi - mosdepth_quantized_bed = COVERAGE.out.mosdepth_quantized_bed - mosdepth_quantized_csi = COVERAGE.out.mosdepth_quantized_csi - mosdepth_thresholds_bed = COVERAGE.out.mosdepth_thresholds_bed - mosdepth_thresholds_csi = COVERAGE.out.mosdepth_thresholds_csi - samtools_coverage = COVERAGE.out.samtools_coverage - panelcoverage = COVERAGE.out.panelcoverage - samtools_stats = BAM_QC.out.samtools_stats - samtools_flagstat = BAM_QC.out.samtools_flagstat - samtools_idxstats = BAM_QC.out.samtools_idxstats - picard_multiplemetrics = BAM_QC.out.picard_multiplemetrics - picard_multiplemetrics_pdf = BAM_QC.out.picard_multiplemetrics_pdf - picard_wgsmetrics = BAM_QC.out.picard_wgsmetrics - picard_hsmetrics = BAM_QC.out.picard_hsmetrics - md5sums = MD5SUM.out.checksum - multiqcsav_report = MULTIQCSAV.out.report.toList() - multiqcsav_data = MULTIQCSAV.out.data.toList() - multiqcsav_plots = MULTIQCSAV.out.plots.toList() - multiqc_report = MULTIQC.out.report - multiqc_data = MULTIQC.out.data - multiqc_plots = MULTIQC.out.plots + demultiplex_interop = BCLCONVERT.out.interop + fastq = ch_fastq_per_sample.other + falco_html = FALCO.out.html + falco_txt = FALCO.out.txt + fastp_json = FASTP.out.json + fastp_html = FASTP.out.html + crams = FASTQ_TO_CRAM.out.cram_crai + rna_splice_junctions = FASTQ_TO_CRAM.out.rna_splice_junctions + rna_junctions = FASTQ_TO_CRAM.out.rna_junctions + align_reports = FASTQ_TO_CRAM.out.align_reports + sormadup_metrics = FASTQ_TO_CRAM.out.sormadup_metrics + mosdepth_global = BAM_QC.out.mosdepth_global + mosdepth_summary = BAM_QC.out.mosdepth_summary + mosdepth_regions = BAM_QC.out.mosdepth_regions + mosdepth_per_base_d4 = BAM_QC.out.mosdepth_per_base_d4 + mosdepth_per_base_bed = BAM_QC.out.mosdepth_per_base_bed + mosdepth_per_base_csi = BAM_QC.out.mosdepth_per_base_csi + mosdepth_regions_bed = BAM_QC.out.mosdepth_regions_bed + mosdepth_regions_csi = BAM_QC.out.mosdepth_regions_csi + mosdepth_quantized_bed = BAM_QC.out.mosdepth_quantized_bed + mosdepth_quantized_csi = BAM_QC.out.mosdepth_quantized_csi + mosdepth_thresholds_bed = BAM_QC.out.mosdepth_thresholds_bed + mosdepth_thresholds_csi = BAM_QC.out.mosdepth_thresholds_csi + samtools_coverage = BAM_QC.out.samtools_coverage + panelcoverage = BAM_QC.out.panelcoverage + samtools_stats = BAM_QC.out.samtools_stats + samtools_flagstat = BAM_QC.out.samtools_flagstat + samtools_idxstats = BAM_QC.out.samtools_idxstats + riker_alignment_metrics = BAM_QC.out.riker_alignment_metrics + riker_base_dist = BAM_QC.out.riker_base_dist + riker_mean_qual = BAM_QC.out.riker_mean_qual + riker_qual_dist = BAM_QC.out.riker_qual_dist + riker_error_mismatch = BAM_QC.out.riker_error_mismatch + riker_error_overlap = BAM_QC.out.riker_error_overlap + riker_error_indel = BAM_QC.out.riker_error_indel + riker_gcbias_detail = BAM_QC.out.riker_gcbias_detail + riker_gcbias_summary = BAM_QC.out.riker_gcbias_summary + riker_hybcap_metrics = BAM_QC.out.riker_hybcap_metrics + riker_hybcap_per_target = BAM_QC.out.riker_hybcap_per_target + riker_hybcap_per_base = BAM_QC.out.riker_hybcap_per_base + riker_isize_metrics = BAM_QC.out.riker_isize_metrics + riker_isize_histogram = BAM_QC.out.riker_isize_histogram + riker_wgs_metrics = BAM_QC.out.riker_wgs_metrics + riker_wgs_coverage = BAM_QC.out.riker_wgs_coverage + riker_pdf = BAM_QC.out.riker_pdf + riker_rna_biotype = BAM_QC.out.riker_rna_biotype + riker_rna_insert_size_histogram = BAM_QC.out.riker_rna_insert_size_histogram + riker_rna_insert_size = BAM_QC.out.riker_rna_insert_size + riker_rna_metrics = BAM_QC.out.riker_rna_metrics + md5sums = MD5SUM.out.checksum + multiqcsav_report = MULTIQCSAV.out.report.toList() + multiqcsav_data = MULTIQCSAV.out.data.toList() + multiqcsav_plots = MULTIQCSAV.out.plots.toList() + multiqc_report = MULTIQC.out.report + multiqc_data = MULTIQC.out.data + multiqc_plots = MULTIQC.out.plots }