diff --git a/CHANGELOG.md b/CHANGELOG.md index 9f6951b8..80d11fbe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Threaded a combined `[ meta, fasta, fai ]` channel through the alignment subworkflows - 🔧 Add [methurator](https://vibtobilab.github.io/methurator/latest/) as an additional QC tool for both the Bismark and bwa-meth subworkflows. - 🔧 Update the `bwameth/align` and `bwameth/index` modules to bwa-meth 0.2.10 (consistent read-name handling and FASTQ comment-tag propagation upstream) and samtools 1.25 ([#637](https://github.com/nf-core/methylseq/pull/637)) +- 🔧 Update Parabricks to 4.8.0-1 (`parabricks/fq2bam` and `parabricks/fq2bammeth`), samtools to 1.25 and Picard to 3.5.0 in the GPU and bwa-mem alignment paths, with the nf-core modules and subworkflows they use (`fastq_align_dedup_bwameth`, `fastq_align_dedup_bwamem`, `fastq_align_bwa`, `bam_sort_stats_samtools`, `bam_stats_samtools`, `bam_methyldackel`). `samtools/faidx` moves to samtools 1.25 too. Results are unchanged, except that Parabricks 4.8 `fq2bam` adds the `MC` tag to unmapped reads with a mapped mate. A new GPU test covers `--aligner bwamem --taps` (`parabricks/fq2bam`) - 🔄 Update template to nf-core/tools v4.2.1 (includes v4.1.0); minimum Nextflow version is now 25.10.4 and nf-schema is bumped to 2.7.3 ([#634](https://github.com/nf-core/methylseq/pull/634)) - 🔧 Merge the nf-core/tools v4.0.2 template; drops the Slack/Teams webhook notification feature (`imNotification`/`hook_url`) in line with the template ([#606](https://github.com/nf-core/methylseq/pull/606)) diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index afca8152..fd7f430d 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { conda = 'modules/nf-core/bwameth/align/.co process { withName: 'BWAMETH_INDEX' { conda = 'modules/nf-core/bwameth/index/.conda-lock/linux_amd64-bd-a589797f382631bc_1.txt' } } process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } } process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { conda = 'modules/nf-core/picard/addorreplacereadgroups/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt' } } +process { withName: 'PICARD_MARKDUPLICATES' { conda = 'modules/nf-core/picard/markduplicates/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt' } } process { withName: 'RASTAIR2_CALL' { conda = 'modules/nf-core/rastair2/call/.conda-lock/linux_amd64-bd-4ffd26b40813e268_1.txt' } } process { withName: 'RASTAIR2_MBIAS' { conda = 'modules/nf-core/rastair2/mbias/.conda-lock/linux_amd64-bd-4ffd26b40813e268_1.txt' } } +process { withName: 'SAMTOOLS_FAIDX' { conda = 'modules/nf-core/samtools/faidx/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { conda = 'modules/nf-core/samtools/flagstat/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } } +process { withName: 'SAMTOOLS_IDXSTATS' { conda = 'modules/nf-core/samtools/idxstats/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } } +process { withName: 'SAMTOOLS_INDEX' { conda = 'modules/nf-core/samtools/index/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } } +process { withName: 'SAMTOOLS_SORT' { conda = 'modules/nf-core/samtools/sort/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } } +process { withName: 'SAMTOOLS_STATS' { conda = 'modules/nf-core/samtools/stats/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index 190b1408..50052615 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { conda = 'modules/nf-core/bwameth/align/.co process { withName: 'BWAMETH_INDEX' { conda = 'modules/nf-core/bwameth/index/.conda-lock/linux_arm64-bd-d9a640227e3efef9_1.txt' } } process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } } process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { conda = 'modules/nf-core/picard/addorreplacereadgroups/.conda-lock/linux_arm64-bd-5516268008db5ab4_1.txt' } } +process { withName: 'PICARD_MARKDUPLICATES' { conda = 'modules/nf-core/picard/markduplicates/.conda-lock/linux_arm64-bd-5516268008db5ab4_1.txt' } } process { withName: 'RASTAIR2_CALL' { conda = 'modules/nf-core/rastair2/call/.conda-lock/linux_arm64-bd-0f7189390ccfdc4d_1.txt' } } process { withName: 'RASTAIR2_MBIAS' { conda = 'modules/nf-core/rastair2/mbias/.conda-lock/linux_arm64-bd-0f7189390ccfdc4d_1.txt' } } +process { withName: 'SAMTOOLS_FAIDX' { conda = 'modules/nf-core/samtools/faidx/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { conda = 'modules/nf-core/samtools/flagstat/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } } +process { withName: 'SAMTOOLS_IDXSTATS' { conda = 'modules/nf-core/samtools/idxstats/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } } +process { withName: 'SAMTOOLS_INDEX' { conda = 'modules/nf-core/samtools/index/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } } +process { withName: 'SAMTOOLS_SORT' { conda = 'modules/nf-core/samtools/sort/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } } +process { withName: 'SAMTOOLS_STATS' { conda = 'modules/nf-core/samtools/stats/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index 114c6fa4..cef5bb77 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'community.wave.seqera.io/libr process { withName: 'BWAMETH_INDEX' { container = 'community.wave.seqera.io/library/bwameth:0.2.10--a589797f382631bc' } } process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } } process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d' } } process { withName: 'RASTAIR2_CALL' { container = 'community.wave.seqera.io/library/htslib_rastair:4ffd26b40813e268' } } process { withName: 'RASTAIR2_MBIAS' { container = 'community.wave.seqera.io/library/htslib_rastair:4ffd26b40813e268' } } +process { withName: 'SAMTOOLS_FAIDX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } } +process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } } +process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index c825984b..8bdd109d 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'community.wave.seqera.io/libr process { withName: 'BWAMETH_INDEX' { container = 'community.wave.seqera.io/library/bwameth:0.2.10--d9a640227e3efef9' } } process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } } process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'community.wave.seqera.io/library/picard:3.5.0--5516268008db5ab4' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.5.0--5516268008db5ab4' } } process { withName: 'RASTAIR2_CALL' { container = 'community.wave.seqera.io/library/htslib_rastair:0f7189390ccfdc4d' } } process { withName: 'RASTAIR2_MBIAS' { container = 'community.wave.seqera.io/library/htslib_rastair:0f7189390ccfdc4d' } } +process { withName: 'SAMTOOLS_FAIDX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } } +process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } } +process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index 3bc0f7da..44a28a56 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'https://community-cr-prod.seq process { withName: 'BWAMETH_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/44/4405ebf9fd0b415a9e28b0cb503b11af0e86c88ab335b098ff4cf48f8f0162e1/data' } } process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } } process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data' } } process { withName: 'RASTAIR2_CALL' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50c87ecbec7ea76f99ff4ad84e16f083c0b74651bf813d9158b1004234f6feca/data' } } process { withName: 'RASTAIR2_MBIAS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50c87ecbec7ea76f99ff4ad84e16f083c0b74651bf813d9158b1004234f6feca/data' } } +process { withName: 'SAMTOOLS_FAIDX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } } +process { withName: 'SAMTOOLS_SORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } } +process { withName: 'SAMTOOLS_STATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index c6d44964..055e7b09 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'https://community-cr-prod.seq process { withName: 'BWAMETH_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/12bda1a46bacec84b4724f48b09117afc6e68a40c59d442bb874c638e19ee571/data' } } process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } } process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/35/35ed881e77f6b66f1b9204394c8909fd66da367891434a81f536704a13fad3c3/data' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/35/35ed881e77f6b66f1b9204394c8909fd66da367891434a81f536704a13fad3c3/data' } } process { withName: 'RASTAIR2_CALL' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/11/11261c0ef97d532effc21421bd7c824749330dba152db93e4d5d583c362e0620/data' } } process { withName: 'RASTAIR2_MBIAS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/11/11261c0ef97d532effc21421bd7c824749330dba152db93e4d5d583c362e0620/data' } } +process { withName: 'SAMTOOLS_FAIDX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } } +process { withName: 'SAMTOOLS_SORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } } +process { withName: 'SAMTOOLS_STATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index 20b2bfb5..c918e5dd 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'oras://community.wave.seqera. process { withName: 'BWAMETH_INDEX' { container = 'oras://community.wave.seqera.io/library/bwameth:0.2.10--77efa7670825aae0' } } process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } } process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--89375ac386b71342' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--89375ac386b71342' } } process { withName: 'RASTAIR2_CALL' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:8f58b5250bf317c8' } } process { withName: 'RASTAIR2_MBIAS' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:8f58b5250bf317c8' } } +process { withName: 'SAMTOOLS_FAIDX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } } +process { withName: 'SAMTOOLS_SORT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } } +process { withName: 'SAMTOOLS_STATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index 46f959d0..25edd381 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'oras://community.wave.seqera. process { withName: 'BWAMETH_INDEX' { container = 'oras://community.wave.seqera.io/library/bwameth:0.2.10--449d0d6bffe0d0ea' } } process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } } process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } +process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--51fe15653ca25a7c' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--51fe15653ca25a7c' } } process { withName: 'RASTAIR2_CALL' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:42892508b9c8b619' } } process { withName: 'RASTAIR2_MBIAS' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:42892508b9c8b619' } } +process { withName: 'SAMTOOLS_FAIDX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } } +process { withName: 'SAMTOOLS_SORT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } } +process { withName: 'SAMTOOLS_STATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } } diff --git a/modules.json b/modules.json index 035c5b7b..ce21265d 100644 --- a/modules.json +++ b/modules.json @@ -57,7 +57,7 @@ }, "bwa/mem": { "branch": "master", - "git_sha": "2fb127c8fd13de0adaa676df7169131e45c0b114", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": ["fastq_align_bwa"] }, "bwamem3/index": { @@ -107,12 +107,12 @@ }, "methyldackel/extract": { "branch": "master", - "git_sha": "f8eeebe6800a0a501ca1dc426b8057c3965047d5", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"] }, "methyldackel/mbias": { "branch": "master", - "git_sha": "f8eeebe6800a0a501ca1dc426b8057c3965047d5", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"] }, "multiqc": { @@ -122,17 +122,17 @@ }, "parabricks/fq2bam": { "branch": "master", - "git_sha": "f0b0dc3c3f001b1b7bf814a3c353baecbab17ea1", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": ["fastq_align_dedup_bwamem"] }, "parabricks/fq2bammeth": { "branch": "master", - "git_sha": "f0b0dc3c3f001b1b7bf814a3c353baecbab17ea1", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": ["fastq_align_dedup_bwameth"] }, "picard/addorreplacereadgroups": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": ["fastq_align_dedup_bwamem"] }, "picard/bedtointervallist": { @@ -152,7 +152,7 @@ }, "picard/markduplicates": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": [ "fastq_align_dedup_bwamem", "fastq_align_dedup_bwamem3", @@ -206,22 +206,22 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "80eb474060aa4aa6d7b4b00e0dc785174f156a28", "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "80eb474060aa4aa6d7b4b00e0dc785174f156a28", "installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "80eb474060aa4aa6d7b4b00e0dc785174f156a28", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "80eb474060aa4aa6d7b4b00e0dc785174f156a28", "installed_by": [ "bam_sort_stats_samtools", "fastq_align_dedup_bismark", @@ -232,7 +232,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "80eb474060aa4aa6d7b4b00e0dc785174f156a28", "installed_by": [ "bam_sort_stats_samtools", "fastq_align_dedup_bismark", @@ -241,7 +241,7 @@ }, "samtools/stats": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "80eb474060aa4aa6d7b4b00e0dc785174f156a28", "installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"] }, "trimgalore": { @@ -260,17 +260,17 @@ "nf-core": { "bam_methyldackel": { "branch": "master", - "git_sha": "f8eeebe6800a0a501ca1dc426b8057c3965047d5", + "git_sha": "984af83497f42f8ed5f9f2c5acbb775f8e928f02", "installed_by": ["subworkflows"] }, "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", + "git_sha": "a582d5633f7df32396681ef4458068e2b509ca91", "installed_by": ["fastq_align_bwa", "fastq_align_dedup_bwamem"] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205", + "git_sha": "a582d5633f7df32396681ef4458068e2b509ca91", "installed_by": ["bam_sort_stats_samtools", "fastq_align_dedup_bwamem3"] }, "bam_taps_conversion": { @@ -291,7 +291,7 @@ }, "fastq_align_bwa": { "branch": "master", - "git_sha": "cbb7a6362981f07d2c26e43f8186025320569ffd", + "git_sha": "7b3452a23773f687ededb4befd037920e5a51341", "installed_by": ["fastq_align_dedup_bwamem"] }, "fastq_align_dedup_bismark": { @@ -301,7 +301,7 @@ }, "fastq_align_dedup_bwamem": { "branch": "master", - "git_sha": "cbb7a6362981f07d2c26e43f8186025320569ffd", + "git_sha": "a582d5633f7df32396681ef4458068e2b509ca91", "installed_by": ["subworkflows"] }, "fastq_align_dedup_bwamem3": { @@ -311,7 +311,7 @@ }, "fastq_align_dedup_bwameth": { "branch": "master", - "git_sha": "d1e879f0959ce1be59f014e0ad6d2f50b08f1172", + "git_sha": "a582d5633f7df32396681ef4458068e2b509ca91", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index bde6a9a3..ab1ebeb1 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process BWA_MEM { tag "$meta.id" label 'process_high' diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index f97e3a9d..5f4a6f61 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process METHYLDACKEL_EXTRACT { tag "$meta.id" label 'process_medium' diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index bb0ac7f1..cef3f9c6 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process METHYLDACKEL_MBIAS { tag "$meta.id" label 'process_low' diff --git a/modules/nf-core/parabricks/fq2bam/main.nf b/modules/nf-core/parabricks/fq2bam/main.nf index 5f78b4db..00354c32 100644 --- a/modules/nf-core/parabricks/fq2bam/main.nf +++ b/modules/nf-core/parabricks/fq2bam/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process PARABRICKS_FQ2BAM { tag "${meta.id}" label 'process_high' @@ -5,14 +8,14 @@ process PARABRICKS_FQ2BAM { // needed by the module to run on a cluster because we need to copy the fasta reference, see https://github.com/nf-core/modules/issues/9230 stageInMode 'copy' - container "nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1" + container "nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1" input: tuple val(meta), path(reads) tuple val(meta2), path(fasta) tuple val(meta3), path(index) tuple val(meta4), path(intervals) - tuple val(meta5), path(known_sites) + tuple val(meta5), path(known_sites), path(known_sites_index) val output_fmt output: diff --git a/modules/nf-core/parabricks/fq2bam/meta.yml b/modules/nf-core/parabricks/fq2bam/meta.yml index a84dc0bf..d3cfefb3 100644 --- a/modules/nf-core/parabricks/fq2bam/meta.yml +++ b/modules/nf-core/parabricks/fq2bam/meta.yml @@ -68,6 +68,12 @@ input: ontologies: - edam: "http://edamontology.org/format_3016" # VCF - edam: "http://edamontology.org/format_3989" # GZIP + - known_sites_index: + type: file + description: (optional) known sites file(s) index for calculating BQSR. markdups + must be true to perform BQSR. + pattern: "*.vcf.gz.tbi" + ontologies: [] - output_fmt: type: string description: Output format for the alignment. Options are 'bam' or 'cram' diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test index 600b054c..a8c9758d 100644 --- a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test +++ b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test @@ -57,10 +57,7 @@ nextflow_process { when { params { - module_args = '--low-memory' - // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6 - // Parabricks’s fq2bam requires 24GB of memory. - // Using --low-memory for testing + module_args = '' bwa_prefix = 'genome.fa' } process { @@ -77,7 +74,7 @@ nextflow_process { ]) input[2] = BWA_INDEX.out.index input[3] = [ [], [] ] - input[4] = [ [], [] ] + input[4] = [ [], [], [] ] input[5] = 'bam' """ } @@ -118,7 +115,7 @@ nextflow_process { ]) input[2] = BWA_INDEX.out.index input[3] = [ [], [] ] - input[4] = [ [], [] ] + input[4] = [ [], [], [] ] input[5] = 'bam' """ } @@ -139,10 +136,7 @@ nextflow_process { when { params { - module_args = '--low-memory' - // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6 - // Parabricks’s fq2bam requires 24GB of memory. - // Using --low-memory for testing + module_args = '' bwa_prefix = 'genome.fasta' } process { @@ -160,7 +154,7 @@ nextflow_process { ]) input[2] = BWA_INDEX_PE.out.index input[3] = [ [], [] ] - input[4] = [ [], [] ] + input[4] = [ [], [], [] ] input[5] = 'bam' """ } @@ -203,7 +197,7 @@ nextflow_process { ]) input[2] = BWA_INDEX_PE.out.index input[3] = [ [], [] ] - input[4] = [ [], [] ] + input[4] = [ [], [], [] ] input[5] = 'bam' """ } @@ -225,10 +219,7 @@ nextflow_process { when { params { - module_args = '--low-memory' - // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6 - // Parabricks’s fq2bam requires 24GB of memory. - // Using --low-memory for testing + module_args = '' bwa_prefix = 'genome.fasta' } process { @@ -242,7 +233,7 @@ nextflow_process { input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[2] = BWA_INDEX_CRAM.out.index input[3] = [ [], [] ] - input[4] = [ [], [] ] + input[4] = [ [], [], [] ] input[5] = 'cram' """ } @@ -289,7 +280,7 @@ nextflow_process { ]) input[2] = BWA_INDEX_PE.out.index input[3] = [ [], [] ] - input[4] = [ [], [] ] + input[4] = [ [], [], [] ] input[5] = 'cram' """ } diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap index 73b7d9f7..5b02b0e4 100644 --- a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap @@ -36,13 +36,13 @@ ], "7": [ - "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e" + "compatible_versions.yml:md5,1d35aeb637782af709d93ba821b41ae0" ], "8": [ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ], "bai": [ @@ -67,7 +67,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e" + "compatible_versions.yml:md5,1d35aeb637782af709d93ba821b41ae0" ], "crai": [ @@ -85,21 +85,21 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] }, { "PARABRICKS_FQ2BAM": null, - "pbrun_version": "4.6.0-1", - "compatible_with": "BWA mem: 0.7.15, Picard: 2.18.25" + "pbrun_version": "4.8.0-1", + "compatible_with": "BWA mem: 0.7.17, Picard: 2.18.25" } ], + "timestamp": "2026-10-22T07:08:10.586645011", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T11:51:22.101975336" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 - fastq - pe - stub": { "content": [ @@ -138,13 +138,13 @@ ], "7": [ - "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e" + "compatible_versions.yml:md5,1d35aeb637782af709d93ba821b41ae0" ], "8": [ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ], "bai": [ @@ -169,7 +169,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e" + "compatible_versions.yml:md5,1d35aeb637782af709d93ba821b41ae0" ], "crai": [ @@ -187,21 +187,21 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] }, { "PARABRICKS_FQ2BAM": null, - "pbrun_version": "4.6.0-1", - "compatible_with": "BWA mem: 0.7.15, Picard: 2.18.25" + "pbrun_version": "4.8.0-1", + "compatible_with": "BWA mem: 0.7.17, Picard: 2.18.25" } ], + "timestamp": "2026-10-22T07:08:56.686755845", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T11:52:38.615055251" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 - fastq - pe": { "content": [ @@ -212,16 +212,16 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] } ], + "timestamp": "2026-10-22T07:08:47.253502764", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T12:29:24.616538827" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 - fastq - se - cram": { "content": [ @@ -232,16 +232,16 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] } ], + "timestamp": "2026-10-22T07:09:33.475180041", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T12:30:46.751327892" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 - fastq - pe - cram - stub": { "content": [ @@ -280,13 +280,13 @@ ], "7": [ - "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e" + "compatible_versions.yml:md5,1d35aeb637782af709d93ba821b41ae0" ], "8": [ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ], "bai": [ @@ -299,7 +299,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e" + "compatible_versions.yml:md5,1d35aeb637782af709d93ba821b41ae0" ], "crai": [ [ @@ -329,16 +329,16 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] } ], + "timestamp": "2026-10-22T07:09:42.96586892", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T11:53:57.062676203" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "SRR389222 - fastq - se": { "content": [ @@ -349,15 +349,15 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] } ], + "timestamp": "2026-10-22T07:08:00.470344317", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T12:28:06.92232134" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file diff --git a/modules/nf-core/parabricks/fq2bam/tests/nextflow.config b/modules/nf-core/parabricks/fq2bam/tests/nextflow.config index 20585ddc..6b5a6b5d 100644 --- a/modules/nf-core/parabricks/fq2bam/tests/nextflow.config +++ b/modules/nf-core/parabricks/fq2bam/tests/nextflow.config @@ -1,11 +1,17 @@ process { withName: 'PARABRICKS_FQ2BAM' { - ext.args = params.module_args + ext.args = { params.module_args } + // The nf-test config caps system memory usage to 4.GB + // This module requires at least 15 GB to run without error + // Note: The Github runners run GPU tests on a machine with 15.1 GB available memory + // See .github/workflows/nf-test-gpu.yml for exact machine specs + memory = 15.GB + accelerator = [request: 1] } withName: 'BWA_INDEX' { - ext.prefix = params.bwa_prefix + ext.prefix = { params.bwa_prefix } } } diff --git a/modules/nf-core/parabricks/fq2bammeth/main.nf b/modules/nf-core/parabricks/fq2bammeth/main.nf index 613cf7d7..f030573f 100644 --- a/modules/nf-core/parabricks/fq2bammeth/main.nf +++ b/modules/nf-core/parabricks/fq2bammeth/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process PARABRICKS_FQ2BAMMETH { tag "${meta.id}" label 'process_high' @@ -5,7 +8,7 @@ process PARABRICKS_FQ2BAMMETH { // needed by the module to work properly can be removed when fixed upstream - see: https://github.com/nf-core/modules/issues/7226 stageInMode 'copy' - container "nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1" + container "nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test index 04daca9f..039a2b0e 100644 --- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test +++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test @@ -29,6 +29,8 @@ nextflow_process { test("SRR389222 single-end [fastq]") { + config './nextflow.config' + when { process { """ diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap index 215714b6..cf11bf92 100644 --- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap @@ -33,7 +33,7 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ], "bai": [ @@ -67,16 +67,16 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] } ], + "timestamp": "2026-10-22T06:54:34.310518694", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T12:22:26.776450379" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "SRR389222 single-end [fastq] - stub": { "content": [ @@ -112,7 +112,7 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ], "bai": [ @@ -146,16 +146,16 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] } ], + "timestamp": "2026-10-22T06:54:24.115500335", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T12:22:10.673464034" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "SRR389222 single-end [fastq]": { "content": [ @@ -174,15 +174,15 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.6.0-1" + "4.8.0-1" ] ] } ], + "timestamp": "2026-10-22T06:54:14.239606526", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-21T12:21:55.454670913" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/nextflow.config b/modules/nf-core/parabricks/fq2bammeth/tests/nextflow.config index 588d8aa8..9aa46e68 100644 --- a/modules/nf-core/parabricks/fq2bammeth/tests/nextflow.config +++ b/modules/nf-core/parabricks/fq2bammeth/tests/nextflow.config @@ -1,8 +1,10 @@ process { withName: 'PARABRICKS_FQ2BAMMETH' { - ext.args = '--low-memory' + // The nf-test config caps system memory usage to 4.GB + // This module requires at least 15 GB to run without error + // Note: The Github runners run GPU tests on a machine with 15.1 GB available memory + // See .github/workflows/nf-test-gpu.yml for exact machine specs + memory = 15.GB + accelerator = [request: 1] } - // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6 - // Parabricks’s fq2bam requires 24GB of memory. - 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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data' + : 'community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d'}" input: tuple val(meta), path(reads) @@ -23,7 +26,7 @@ process PICARD_ADDORREPLACEREADGROUPS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def suffix = reads.getExtension() def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { @@ -48,7 +51,7 @@ process PICARD_ADDORREPLACEREADGROUPS { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def suffix = reads.getExtension() if ("${reads}" == "${prefix}.${suffix}") { error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") } diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index 907c401d..0e5f1845 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -109,3 +109,27 @@ maintainers: - "@hseabolt" - "@cmatKhan" - "@muffato" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d + build_id: bd-be20f299a1924f0d_1 + scan_id: sc-ad63bee994dd89b0_1 + linux/arm64: + name: community.wave.seqera.io/library/picard:3.5.0--5516268008db5ab4 + build_id: bd-5516268008db5ab4_1 + scan_id: sc-c16455a3c81bb32a_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/picard:3.5.0--89375ac386b71342 + build_id: bd-89375ac386b71342_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data + linux/arm64: + name: oras://community.wave.seqera.io/library/picard:3.5.0--51fe15653ca25a7c + build_id: bd-51fe15653ca25a7c_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/35/35ed881e77f6b66f1b9204394c8909fd66da367891434a81f536704a13fad3c3/data + conda: + linux/amd64: + lock_file: modules/nf-core/picard/addorreplacereadgroups/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt + linux/arm64: + lock_file: modules/nf-core/picard/addorreplacereadgroups/.conda-lock/linux_arm64-bd-5516268008db5ab4_1.txt diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config index 132cc0f7..55436933 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config @@ -1,12 +1,8 @@ process { - withName: 'PICARD_ADDORREPLACEREADGROUPS'{ - ext.prefix = { "${meta.id}.replaced"} - ext.args = {[ - "--CREATE_INDEX", - "-LB ${meta.id}", - "-PL ILLUMINA", - "-PU bc1", - "-SM ${meta.id}" - ].join(' ').trim()} + withName: PICARD_ADDORREPLACEREADGROUPS { + ext.prefix = { "${meta.id}.replaced" } + ext.args = { + ["--CREATE_INDEX", "-LB ${meta.id}", "-PL ILLUMINA", "-PU bc1", "-SM ${meta.id}"].join(' ').trim() + } } } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config index be92e72b..27afb470 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config @@ -1,12 +1,8 @@ process { - withName: 'PICARD_ADDORREPLACEREADGROUPS'{ - ext.prefix = { "${meta.id}.replaced"} - ext.args = {[ - "-LB ${meta.id}", - "-PL ILLUMINA", - "-PU bc1", - "-SM ${meta.id}" - ].join(' ').trim()} - ext.suffix = { "cram" } + withName: PICARD_ADDORREPLACEREADGROUPS { + ext.prefix = { "${meta.id}.replaced" } + ext.args = { + ["-LB ${meta.id}", "-PL ILLUMINA", "-PU bc1", "-SM ${meta.id}"].join(' ').trim() + } } } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test index 78565882..3eade374 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { when { process { """ - input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] + input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [ [:], [], [] ] """ } @@ -26,7 +26,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.bam[0][1]).name, + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, file(process.out.bai[0][1]).name, process.out.findAll { key, val -> key.startsWith("versions") } ).match()} @@ -40,21 +40,18 @@ nextflow_process { when { process { """ - input[0] = [ - [ id:'test' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), ] - ] + input[0] = [ [ id:'test' ],[file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)] ] input[1] = [ [:], 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 { + def fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta' assertAll( { assert process.success }, { assert snapshot( - file(process.out.cram[0][1]).name, + process.out.cram.collect{meta, cram_ -> file(cram_).name + ':readsMD5,' + cram(cram_, fasta).getReadsMD5()}, process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) @@ -67,7 +64,7 @@ nextflow_process { when { process { """ - input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] + input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [ [:], [], [] ] """ } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index 17295697..d4274c70 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -1,22 +1,24 @@ { "homo_sapiens - cram": { "content": [ - "test.replaced.cram", + [ + "test.replaced.cram:readsMD5,2f11e4fe3390b8ad0a1852616fd1da04" + ], { "versions_picard": [ [ "PICARD_ADDORREPLACEREADGROUPS", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-08-19T15:27:33.985055", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:16.966842212" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 - bam - stub": { "content": [ @@ -27,9 +29,9 @@ "bam": [ [ { - + "id": "test" }, - "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "cram": [ @@ -39,35 +41,37 @@ [ "PICARD_ADDORREPLACEREADGROUPS", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-08-20T09:32:59.890631", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-02-19T17:34:40.3572859" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 - bam": { "content": [ - "null.replaced.bam", - "null.replaced.bai", + [ + "test.replaced.bam:readsMD5,894549ee3ced6b5ca2eed2563a985217" + ], + "test.replaced.bai", { "versions_picard": [ [ "PICARD_ADDORREPLACEREADGROUPS", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-08-20T09:32:27.740178", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:00.935196996" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt b/modules/nf-core/picard/markduplicates/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt new file mode 100644 index 00000000..8b5bdf78 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt @@ -0,0 +1,1298 @@ +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 + - 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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' - : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data' + : 'community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d'}" input: tuple val(meta), path(reads) @@ -24,7 +27,7 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def suffix = reads.getExtension() def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { @@ -50,7 +53,7 @@ process PICARD_MARKDUPLICATES { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def suffix = reads.getExtension() if ("${reads}" == "${prefix}.${suffix}") { error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") } diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index cf95a0c5..16e1223e 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -62,8 +62,7 @@ output: e.g. [ id:'test', single_end:false ] - "*.bai": type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be - passed as a flag + description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag pattern: "*.{bai}" ontologies: [] cram: @@ -117,3 +116,27 @@ maintainers: - "@drpatelh" - "@projectoriented" - "@ramprasadn" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/picard:3.5.0--5516268008db5ab4 + build_id: bd-5516268008db5ab4_1 + scan_id: sc-c16455a3c81bb32a_1 + linux/amd64: + name: community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d + build_id: bd-be20f299a1924f0d_1 + scan_id: sc-ad63bee994dd89b0_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/picard:3.5.0--51fe15653ca25a7c + build_id: bd-51fe15653ca25a7c_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/35/35ed881e77f6b66f1b9204394c8909fd66da367891434a81f536704a13fad3c3/data + linux/amd64: + name: oras://community.wave.seqera.io/library/picard:3.5.0--89375ac386b71342 + build_id: bd-89375ac386b71342_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data + conda: + linux/amd64: + lock_file: modules/nf-core/picard/markduplicates/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt + linux/arm64: + lock_file: modules/nf-core/picard/markduplicates/.conda-lock/linux_arm64-bd-5516268008db5ab4_1.txt diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index 227bfc84..f04a8622 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -27,7 +27,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.bam[0][1]).name, + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, path(process.out.metrics.get(0).get(1)).readLines()[0..2], process.out.findAll { key, val -> key.startsWith("versions") }) .match() } @@ -53,7 +53,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.bam[0][1]).name, + process.out.bam.collect{meta, bam_ -> file(bam_).name + ':readsMD5,' + bam(bam_).getReadsMD5()}, path(process.out.metrics.get(0).get(1)).readLines()[0..2], process.out.findAll { key, val -> key.startsWith("versions") }) .match() } @@ -80,13 +80,14 @@ nextflow_process { } then { + def fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta' assertAll( { assert process.success }, { assert snapshot( - file(process.out.cram[0][1]).name, + process.out.cram.collect{meta, cram_ -> file(cram_).name + ':readsMD5,' + cram(cram_, fasta).getReadsMD5()}, path(process.out.metrics.get(0).get(1)).readLines()[0..2], - process.out.findAll { key, val -> key.startsWith("versions") }) - .match() } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 261f1d5f..5c8948a1 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -36,16 +36,16 @@ [ "PICARD_MARKDUPLICATES", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-02-19T17:43:13.544887277", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-19T17:43:13.544887277" + } }, "sarscov2 [unsorted bam] - stub": { "content": [ @@ -84,20 +84,22 @@ [ "PICARD_MARKDUPLICATES", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-02-19T17:43:06.193033248", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-19T17:43:06.193033248" + } }, "sarscov2 [unsorted bam]": { "content": [ - "test.md.bam", + [ + "test.md.bam:readsMD5,762e859a3d0ed1553655cde77665c940" + ], [ "## htsjdk.samtools.metrics.StringHeader", "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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", @@ -108,20 +110,22 @@ [ "PICARD_MARKDUPLICATES", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-08-19T18:40:56.948628", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-02-19T17:42:40.574463587" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 [sorted bam]": { "content": [ - "test.md.bam", + [ + "test.md.bam:readsMD5,894549ee3ced6b5ca2eed2563a985217" + ], [ "## htsjdk.samtools.metrics.StringHeader", "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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", @@ -132,20 +136,22 @@ [ "PICARD_MARKDUPLICATES", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-08-19T18:41:17.239873", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-02-19T17:42:49.374645492" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "homo_sapiens [cram]": { "content": [ - "test.md.cram", + [ + "test.md.cram:readsMD5,2f11e4fe3390b8ad0a1852616fd1da04" + ], [ "## htsjdk.samtools.metrics.StringHeader", "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.md.cram --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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", @@ -156,16 +162,16 @@ [ "PICARD_MARKDUPLICATES", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-08-19T18:41:41.238597", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-02-19T17:42:59.07843756" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "homo_sapiens [cram] - stub": { "content": [ @@ -204,15 +210,15 @@ [ "PICARD_MARKDUPLICATES", "picard", - "3.4.0" + "3.5.0" ] ] } ], + "timestamp": "2026-02-19T17:43:20.676018462", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-19T17:43:20.676018462" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config index f8dd0f1c..4d7b42f1 100644 --- a/modules/nf-core/picard/markduplicates/tests/nextflow.config +++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config @@ -1,6 +1,6 @@ process { withName: PICARD_MARKDUPLICATES { ext.prefix = { "${meta.id}.md" } - ext.args = '--ASSUME_SORT_ORDER queryname' + ext.args = '--ASSUME_SORT_ORDER queryname' } } diff --git a/modules/nf-core/samtools/faidx/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt b/modules/nf-core/samtools/faidx/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt new file mode 100644 index 00000000..23c42989 --- /dev/null +++ b/modules/nf-core/samtools/faidx/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt @@ -0,0 +1,350 @@ +version: 6 +environments: + default: + channels: + - 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bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.25 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.25 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 175a53a8..2ce37748 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -1,11 +1,14 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process SAMTOOLS_FAIDX { tag "${fasta}" 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/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4'}" input: tuple val(meta), path(fasta), path(fai) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 529f7a26..2ff0345f 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -1,6 +1,5 @@ name: samtools_faidx -description: Index FASTA file, and optionally generate a file of chromosome - sizes +description: Index FASTA file, and optionally generate a file of chromosome sizes keywords: - index - fasta @@ -15,6 +14,11 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + publication: + author: "Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. & 1000 Genome Project Data Processing Subgroup" + year: 2009 + title: "The Sequence Alignment/Map format and SAMtools" + source: "Bioinformatics" licence: - "MIT" identifier: biotools:samtools @@ -111,3 +115,27 @@ maintainers: - "@maxulysse" - "@phue" - "@matthdsm" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2 + build_id: bd-944a4060c62320c2_8 + scan_id: sc-6655c495363315c2_1 + linux/amd64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4 + build_id: bd-704fb80d75745bd4_7 + scan_id: sc-03641d545f6d3bac_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c + build_id: bd-2d67558d8613e11c_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data + linux/arm64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a + build_id: bd-3b9e70f96c37875a_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data + conda: + linux/amd64: + lock_file: modules/nf-core/samtools/faidx/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt + linux/arm64: + lock_file: modules/nf-core/samtools/faidx/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test index 9a86db86..d6693071 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -31,7 +31,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -57,7 +57,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -83,14 +83,15 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } - test("test_samtools_faidx_stub_fasta") { + test("test_samtools_faidx_fasta - stub") { options "-stub" + when { params { module_args = '-o extract.fa' @@ -110,14 +111,15 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } - test("test_samtools_faidx_stub_fai") { + test("test_samtools_faidx_fai - stub") { options "-stub" + when { params { module_args = '' @@ -137,7 +139,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -163,7 +165,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -189,7 +191,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -217,7 +219,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(sanitizeOutput(process.out)).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -249,5 +251,4 @@ nextflow_process { ) } } - } diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index e879d962..cf36aac5 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -1,4 +1,39 @@ { + "test_samtools_faidx_fasta - stub": { + "content": [ + { + "fa": [ + [ + { + "id": "test" + }, + "extract.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "sizes": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.25" + ] + ] + } + ], + "timestamp": "2026-10-28T07:03:05.017603", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } + }, "test_samtools_faidx": { "content": [ { @@ -23,16 +58,16 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:02:52.7332", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:57:29.747964" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "test_samtools_faidx_get_sizes_bgzip - stub": { "content": [ @@ -68,16 +103,16 @@ [ "SAMTOOLS_FAIDX", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:03:27.235011", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:58:10.04235" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "test_samtools_faidx_get_sizes": { "content": [ @@ -108,16 +143,16 @@ [ "SAMTOOLS_FAIDX", "samtools", - 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bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.25 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.25 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 2d9588b9..32f8a95c 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -1,11 +1,14 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process SAMTOOLS_FLAGSTAT { 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/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4'}" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index f658acdd..48944c2d 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -1,6 +1,5 @@ name: samtools_flagstat -description: Counts the number of alignments in a BAM/CRAM/SAM file for each - FLAG type +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type keywords: - stats - mapping @@ -17,6 +16,11 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + publication: + author: "Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. & 1000 Genome Project Data Processing Subgroup" + year: 2009 + title: "The Sequence Alignment/Map format and SAMtools" + source: "Bioinformatics" licence: - "MIT" identifier: biotools:samtools @@ -74,3 +78,27 @@ authors: maintainers: - "@drpatelh" - "@matthdsm" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4 + build_id: bd-704fb80d75745bd4_7 + scan_id: sc-03641d545f6d3bac_1 + linux/arm64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2 + build_id: bd-944a4060c62320c2_8 + scan_id: sc-6655c495363315c2_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c + build_id: bd-2d67558d8613e11c_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data + linux/arm64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a + build_id: bd-3b9e70f96c37875a_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data + conda: + linux/amd64: + lock_file: modules/nf-core/samtools/flagstat/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt + linux/arm64: + lock_file: modules/nf-core/samtools/flagstat/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt 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..8005563b 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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:04:28.234449", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:59:26.188788" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "BAM": { "content": [ { - 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bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.25 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.25 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 4d74768a..95e5e059 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -1,11 +1,14 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process SAMTOOLS_IDXSTATS { 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/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4'}" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 0f9fb3d7..beefcb4b 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -17,6 +17,11 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + publication: + author: "Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. & 1000 Genome Project Data Processing Subgroup" + year: 2009 + title: "The Sequence Alignment/Map format and SAMtools" + source: "Bioinformatics" licence: - "MIT" identifier: biotools:samtools @@ -74,3 +79,27 @@ authors: maintainers: - "@drpatelh" - "@matthdsm" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4 + build_id: bd-704fb80d75745bd4_7 + scan_id: sc-03641d545f6d3bac_1 + linux/arm64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2 + build_id: bd-944a4060c62320c2_8 + scan_id: sc-6655c495363315c2_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c + build_id: bd-2d67558d8613e11c_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data + linux/arm64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a + build_id: bd-3b9e70f96c37875a_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data + conda: + linux/amd64: + lock_file: modules/nf-core/samtools/idxstats/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt + linux/arm64: + lock_file: modules/nf-core/samtools/idxstats/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt 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..a0aea35c 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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:04:40.510473", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T08:59:41.877526" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "bam": { "content": [ @@ -42,15 +42,15 @@ [ "SAMTOOLS_IDXSTATS", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:04:34.749399", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - 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bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.25 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.25 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 5b5756b1..829d6663 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -1,11 +1,14 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process SAMTOOLS_INDEX { 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/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4'}" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index d4938bcd..edf5afbe 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -14,6 +14,11 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + publication: + author: "Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. & 1000 Genome Project Data Processing Subgroup" + year: 2009 + title: "The Sequence Alignment/Map format and SAMtools" + source: "Bioinformatics" licence: - "MIT" identifier: biotools:samtools @@ -68,3 +73,27 @@ maintainers: - "@ewels" - "@maxulysse" - "@matthdsm" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4 + build_id: bd-704fb80d75745bd4_7 + scan_id: sc-03641d545f6d3bac_1 + linux/arm64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2 + build_id: bd-944a4060c62320c2_8 + scan_id: sc-6655c495363315c2_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c + build_id: bd-2d67558d8613e11c_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data + linux/arm64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a + build_id: bd-3b9e70f96c37875a_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data + conda: + linux/amd64: + lock_file: modules/nf-core/samtools/index/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt + linux/arm64: + lock_file: modules/nf-core/samtools/index/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index f9d39222..d62d2d0f 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -12,7 +12,7 @@ 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) ]) @@ -21,8 +21,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.index, process.out.findAll { key, val -> key.startsWith('versions') } @@ -35,7 +35,7 @@ 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/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) ]) @@ -44,8 +44,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.index, process.out.findAll { key, val -> key.startsWith('versions') } @@ -60,7 +60,7 @@ 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) ]) @@ -69,8 +69,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( file(process.out.index[0][1]).name, process.out.findAll { key, val -> key.startsWith('versions') } @@ -80,11 +80,13 @@ nextflow_process { } test("bai - 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) ]) @@ -93,8 +95,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.index, process.out.findAll { key, val -> key.startsWith('versions') } @@ -104,11 +106,13 @@ nextflow_process { } test("crai - 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/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) ]) @@ -117,8 +121,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.index, process.out.findAll { key, val -> key.startsWith('versions') } @@ -128,13 +132,15 @@ nextflow_process { } test("csi - stub") { + options "-stub" + config "./csi.nextflow.config" 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) ]) @@ -143,8 +149,8 @@ nextflow_process { } then { - assertAll ( - { assert process.success }, + assert process.success + assertAll( { assert snapshot( process.out.index, process.out.findAll { key, val -> key.startsWith('versions') } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 337dec77..7c4f2edf 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -15,16 +15,16 @@ [ "SAMTOOLS_INDEX", "samtools", - 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bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.25 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.25 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index e75ce915..f538c56a 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -1,14 +1,17 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process SAMTOOLS_SORT { 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/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4'}" input: - tuple val(meta), path(bam) + tuple val(meta), path(bam, stageAs: "?/*") tuple val(meta2), path(fasta), path(fai) val index_format diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 0447a95e..94155221 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -14,6 +14,11 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + publication: + author: "Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. & 1000 Genome Project Data Processing Subgroup" + year: 2009 + title: "The Sequence Alignment/Map format and SAMtools" + source: "Bioinformatics" licence: ["MIT"] identifier: biotools:samtools input: @@ -124,3 +129,27 @@ maintainers: - "@drpatelh" - "@ewels" - "@matthdsm" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2 + build_id: bd-944a4060c62320c2_8 + scan_id: sc-6655c495363315c2_1 + linux/amd64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4 + build_id: bd-704fb80d75745bd4_7 + scan_id: sc-03641d545f6d3bac_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c + build_id: bd-2d67558d8613e11c_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data + linux/arm64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a + build_id: bd-3b9e70f96c37875a_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data + conda: + linux/amd64: + lock_file: modules/nf-core/samtools/sort/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt + linux/arm64: + lock_file: modules/nf-core/samtools/sort/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt 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..05a2cd4d 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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:06.285795", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:36.491063" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:08:50.054412", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:14.341977" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "bam - stub": { "content": [ @@ -78,27 +72,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:11.937524", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:43.558376" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:08:58.322127", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:25.647565" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "cram - stub": { "content": [ @@ -132,27 +120,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:19.958217", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:54.684578" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:08:54.247863", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:20.2368" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "multiple bam - stub": { "content": [ @@ -180,51 +162,21 @@ [ "SAMTOOLS_SORT", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:15.980747", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:04:48.874947" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:08:42.162211", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:00.624092" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "multiple bam csi index": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,f168809dc154156c40548c06d0f46791" - 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bioconda dependencies: # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.23.1 + - bioconda::htslib=1.25 # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.23.1 + - bioconda::samtools=1.25 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 28457e68..cc7aa9da 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -1,11 +1,14 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + process SAMTOOLS_STATS { 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/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data' - : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' + : 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4'}" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 5fd7e76d..83be2bf2 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -15,6 +15,11 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + publication: + author: "Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. & 1000 Genome Project Data Processing Subgroup" + year: 2009 + title: "The Sequence Alignment/Map format and SAMtools" + source: "Bioinformatics" licence: ["MIT"] identifier: biotools:samtools input: @@ -92,3 +97,27 @@ maintainers: - "@FriederikeHanssen" - "@ramprasadn" - "@matthdsm" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4 + build_id: bd-704fb80d75745bd4_7 + scan_id: sc-03641d545f6d3bac_1 + linux/arm64: + name: community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2 + build_id: bd-944a4060c62320c2_8 + scan_id: sc-6655c495363315c2_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c + build_id: bd-2d67558d8613e11c_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data + linux/arm64: + name: oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a + build_id: bd-3b9e70f96c37875a_8 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data + conda: + linux/amd64: + lock_file: modules/nf-core/samtools/stats/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt + linux/arm64: + lock_file: modules/nf-core/samtools/stats/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt 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..da5268ee 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,a90e96f17f11946c466139510405e4cc" ] ], "versions_samtools": [ [ "SAMTOOLS_STATS", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:41.215195", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:39.987454" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:45.284167", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:47.495502" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "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" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:49.252669", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:56.38373" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "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:md5,8aee6d59201daa816df33218e176e5e5" ] ], "versions_samtools": [ [ "SAMTOOLS_STATS", "samtools", - "1.23.1" + "1.25" ] ] } ], + "timestamp": "2026-10-28T07:09:37.259343", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:05:24.59441" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_methyldackel/main.nf b/subworkflows/nf-core/bam_methyldackel/main.nf index 943c0b69..3a11cc23 100644 --- a/subworkflows/nf-core/bam_methyldackel/main.nf +++ b/subworkflows/nf-core/bam_methyldackel/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + include { METHYLDACKEL_EXTRACT } from '../../../modules/nf-core/methyldackel/extract/main' include { METHYLDACKEL_MBIAS } from '../../../modules/nf-core/methyldackel/mbias/main' diff --git a/subworkflows/nf-core/bam_methyldackel/meta.yml b/subworkflows/nf-core/bam_methyldackel/meta.yml index 1b659262..ca1e7759 100644 --- a/subworkflows/nf-core/bam_methyldackel/meta.yml +++ b/subworkflows/nf-core/bam_methyldackel/meta.yml @@ -26,24 +26,31 @@ input: Structure: [ val(meta), path(fasta), path(fai) ] pattern: "*.{fa,fa.gz}" output: - - methydackel_extract_bedgraph: + - methyldackel_extract_bedgraph: type: file description: | bedGraph file, containing per-base methylation metrics Structure: [ val(meta), path(bedgraph) ] pattern: "*.bedGraph" - - methydackel_extract_methylkit: + - methyldackel_extract_methylkit: type: file description: | methylKit file, containing per-base methylation metrics Structure: [ val(meta), path(methylKit) ] pattern: "*.methylKit" - - methydackel_mbias: + - methyldackel_mbias: type: file description: | Text file containing methylation bias Structure: [ val(meta), path(mbias) ] pattern: "*.{txt}" + - multiqc: + type: file + description: | + Collected MethylDackel files for use as MultiQC input + + Structure: [ path(files) ] + pattern: "*.{html,txt}" authors: - "@eduard-watchmaker" maintainers: diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf index d0cd8c30..74e85186 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + // // Sort, index BAM file and run samtools stats, flagstat and idxstats // diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml index e01f9ccf..44c1a50d 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml +++ b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml @@ -14,54 +14,63 @@ components: - samtools/flagstat - bam_stats_samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: + - ch_bam: type: file - description: BAM/CRAM/SAM file + description: | + BAM/CRAM/SAM file. + + Structure: [ val(meta), path(bam) ] pattern: "*.{bam,cram,sam}" - - fasta: + + - ch_fasta_fai: type: file - description: Reference genome fasta file + description: | + Reference genome fasta file and its index. + + Structure: [ val(meta), path(fasta), path(fai) ] pattern: "*.{fasta,fa}" -# TODO Update when we decide on a standard for subworkflow docs + output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: type: file - description: Sorted BAM/CRAM/SAM file + description: | + Sorted BAM/CRAM/SAM file. + + Structure: [ val(meta), path(bam) ] pattern: "*.{bam,cram,sam}" - - bai: + + - index: type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + description: | + BAM/CRAM/SAM index file. + + Structure: [ val(meta), path(index) ] + pattern: "*.{bai,crai,csi}" + - stats: type: file - description: File containing samtools stats output - pattern: "*.{stats}" + description: | + File containing samtools stats output. + + Structure: [ val(meta), path(stats) ] + pattern: "*.stats" + - flagstat: type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + description: | + File containing samtools flagstat output. + + Structure: [ val(meta), path(flagstat) ] + pattern: "*.flagstat" + - idxstats: type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + description: | + File containing samtools idxstats output. + + Structure: [ val(meta), path(idxstats) ] + pattern: "*.idxstats" + authors: - "@drpatelh" - "@ewels" diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index 2db95965..aa0ae531 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -8,6 +8,7 @@ nextflow_workflow { tag "subworkflows/bam_sort_stats_samtools" tag "bam_sort_stats_samtools" tag "subworkflows/bam_stats_samtools" + tag "subworkflows/../bam_stats_samtools" tag "bam_stats_samtools" tag "samtools" tag "samtools/index" diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index d2ed2c25..aab1d4bd 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -25,15 +25,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,0d0496957cd3bae8f557f2e9f6876a46" + "test.stats:md5,ffad2f1f5ccfbb948e42cd2cb25aca7d" ] ] ], + "timestamp": "2026-10-28T07:19:52.857822", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:55:29.570804" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "test_bam_sort_stats_samtools_paired_end": { "content": [ @@ -61,15 +61,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,12b526148cc9b6ffa8893903f65f19fc" + "test.stats:md5,8d3a1e1b1bedf370281c848317105545" ] ] ], + "timestamp": "2026-10-28T07:20:00.860575", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T09:55:39.804101" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "test_bam_sort_stats_samtools_single_end - stub": { "content": [ @@ -166,11 +166,11 @@ ] } ], + "timestamp": "2026-03-12T15:01:02.797853", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-12T15:01:02.797853" + } }, "test_bam_sort_stats_samtools_paired_end - stub": { "content": [ @@ -267,10 +267,10 @@ ] } ], + "timestamp": "2026-03-12T15:01:13.722701", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-12T15:01:13.722701" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf index 14545ba2..8303cfae 100644 --- a/subworkflows/nf-core/bam_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + // // Run SAMtools stats, flagstat and idxstats // diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml index 809bf736..fea06778 100644 --- a/subworkflows/nf-core/bam_stats_samtools/meta.yml +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -16,10 +16,10 @@ input: description: | The input channel containing the BAM/CRAM and it's index Structure: [ val(meta), path(bam), path(bai) ] - - ch_fasta: + - ch_fasta_fai: description: | - Reference genome fasta file - Structure: [ path(fasta) ] + Reference genome fasta file and its index + Structure: [ val(meta2), path(fasta), path(fai) ] output: - stats: description: | @@ -33,10 +33,6 @@ output: description: | File containing samtools idxstats output Structure: [ val(meta), path(idxstats)] - - versions: - description: | - Files containing software versions - Structure: [ path(versions.yml) ] authors: - "@drpatelh" maintainers: diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap index 5a4a01f9..17bc1578 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -58,11 +58,11 @@ ] } ], + "timestamp": "2026-02-03T11:10:30.076183827", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T11:10:30.076183827" + } }, "test_bam_stats_samtools_single_end - stub": { "content": [ @@ -123,11 +123,11 @@ ] } ], + "timestamp": "2026-02-03T11:10:24.379362883", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T11:10:24.379362883" + } }, "test_bam_stats_samtools_paired_end_cram - stub": { "content": [ @@ -188,11 +188,11 @@ ] } ], + "timestamp": "2026-02-03T11:10:35.91658956", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T11:10:35.91658956" + } }, "test_bam_stats_samtools_single_end": { "content": [ @@ -220,15 +220,15 @@ "id": "test", "single_end": true }, - "test.stats:md5,afd73326205e0995268b7a796d93139e" + "test.stats:md5,4f6b69a144c8e1d93110b0c6ad961aac" ] ] ], + "timestamp": "2026-10-28T07:20:26.696028", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T10:42:09.4463" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "test_bam_stats_samtools_paired_end": { "content": [ @@ -256,15 +256,15 @@ "id": "test", "single_end": true }, - "test.stats:md5,681ce95af0c57dc36c647f2157c17b6a" + "test.stats:md5,3cdba85eb1287f1f2273eb45b48fcfd9" ] ] ], + "timestamp": "2026-10-28T07:20:32.474522", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T10:42:15.787592" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } }, "test_bam_stats_samtools_paired_end_cram": { "content": [ @@ -292,14 +292,14 @@ "id": "test", "single_end": false }, - "test.stats:md5,96020b0280addb09a48c63a5d510fc15" + "test.stats:md5,f0a64674d746d343f9c9bb2dacfff14d" ] ] ], + "timestamp": "2026-10-28T07:20:38.134112", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-19T10:42:22.199498" + "nf-test": "0.9.5", + "nextflow": "26.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_bwa/main.nf b/subworkflows/nf-core/fastq_align_bwa/main.nf index eb72bade..61db9fd6 100644 --- a/subworkflows/nf-core/fastq_align_bwa/main.nf +++ b/subworkflows/nf-core/fastq_align_bwa/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + // // Alignment with BWA // diff --git a/subworkflows/nf-core/fastq_align_bwa/meta.yml b/subworkflows/nf-core/fastq_align_bwa/meta.yml index 12569fa3..24742251 100644 --- a/subworkflows/nf-core/fastq_align_bwa/meta.yml +++ b/subworkflows/nf-core/fastq_align_bwa/meta.yml @@ -43,14 +43,10 @@ output: description: | BAM file ordered by samtools Structure: [ val(meta), path(bam) ] - - bai: + - index: description: | - BAI index of the ordered BAM file - Structure: [ val(meta), path(bai) ] - - csi: - description: | - CSI index of the ordered BAM file - Structure: [ val(meta), path(csi) ] + Index of the ordered BAM file (bai or csi) + Structure: [ val(meta), path(index) ] - stats: description: | File containing samtools stats output diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf index e910fa5e..a6f15eea 100755 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main' include { FASTQ_ALIGN_BWA } from '../../nf-core/fastq_align_bwa/main' include { PICARD_ADDORREPLACEREADGROUPS } from '../../../modules/nf-core/picard/addorreplacereadgroups/main' @@ -13,7 +16,7 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { use_gpu // boolean: whether to use GPU accelerated alignment output_fmt // string: output format for parabricks fq2bam (e.g., 'bam' or 'cram') interval_file // channel: [ val(meta), [ interval file ] ] - known_sites // channel: [ val(meta), [ known sites ] ] + known_sites // channel: [ val(meta), [ known sites ], [known sites index] ] main: ch_alignment = channel.empty() @@ -23,7 +26,8 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { ch_idxstats = channel.empty() ch_picard_metrics = channel.empty() ch_multiqc_files = channel.empty() - ch_fasta = ch_fasta_fai.map { meta, fasta, _fai -> [meta, fasta] } + // PARABRICKS_FQ2BAM does not use fai + ch_fasta = ch_fasta_fai.map { meta, fasta, _fai -> [ meta, fasta ] } /* Align with parabricks GPU enabled fq2bam implementation of bwa-mem */ diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml index d38dae81..8899f26c 100755 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml @@ -25,15 +25,12 @@ input: respectively. Structure: [ val(meta), [ path(reads) ] ] pattern: "*.{fastq,fastq.gz}" - - ch_fasta: + - ch_fasta_fai: type: file description: | - Structure: [ val(meta), path(fasta) ] + Reference genome fasta file and its index + Structure: [ val(meta), path(fasta), path(fai) ] pattern: "*.{fa,fa.gz}" - - ch_fasta_index: - type: file - description: | - Structure: [ val(meta), path(fasta index) ] - ch_bwamem_index: type: directory description: | @@ -69,11 +66,11 @@ output: Channel containing BAM files Structure: [ val(meta), path(bam) ] pattern: "*.bam" - - bai: + - index: type: file description: | - Channel containing indexed BAM (BAI) files - Structure: [ val(meta), path(bai) ] + Channel containing the index of the aligned BAM (BAI) files + Structure: [ val(meta), path(index) ] pattern: "*.bai" - samtools_flagstat: type: file @@ -81,18 +78,18 @@ output: File containing samtools flagstat output Structure: [ val(meta), path(flagstat) ] pattern: "*.flagstat" - - samtools_idxstats: - type: file - description: | - File containing samtools idxstats output - Structure: [ val(meta), path(idxstats) ] - pattern: "*.idxstats" - samtools_stats: type: file description: | File containing samtools stats output Structure: [ val(meta), path(stats) ] pattern: "*.{stats}" + - samtools_idxstats: + type: file + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats) ] + pattern: "*.idxstats" - picard_metrics: type: file description: | diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config old mode 100644 new mode 100755 index bc1fcf15..da738a80 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config @@ -1,14 +1,13 @@ -// IMPORTANT: This config file should be included to ensure that the subworkflow works properly. -process { - withName: 'SAMTOOLS_SORT' { - ext.prefix = { "${meta.id}.sorted" } - } - withName: 'PICARD_MARKDUPLICATES' { - ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES true --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp" - ext.prefix = { "${meta.id}.deduped.sorted" } - } - withName: 'PICARD_ADDORREPLACEREADGROUPS' { - ext.args = "--RGID 1 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM sample1" - ext.prefix = { "${meta.id}.RG.sorted" } - } -} +process { + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + } + withName: PICARD_MARKDUPLICATES { + ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES true --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp" + ext.prefix = { "${meta.id}.deduped.sorted" } + } + withName: PICARD_ADDORREPLACEREADGROUPS { + ext.args = "--RGID 1 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM sample1" + ext.prefix = { "${meta.id}.RG.sorted" } + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test index 97894bf3..bcf83674 100755 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test @@ -9,21 +9,20 @@ nextflow_workflow { tag "subworkflows" tag "subworkflows_nfcore" tag "subworkflows/fastq_align_dedup_bwamem" - tag "parabricks/fq2bam" - tag "samtools/index" - tag "picard/markduplicates" + tag "bam_sort_stats_samtools" tag "bwa" tag "bwa/index" + tag "parabricks" tag "parabricks/fq2bam" + tag "picard/addorreplacereadgroups" + tag "picard/markduplicates" tag "samtools" - tag "samtools/sort" - tag "samtools/index" - tag "samtools/idxstats" tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/index" + tag "samtools/index" + tag "samtools/sort" tag "samtools/stats" - tag "bam_sort_stats_samtools" - tag "picard/markduplicates" - tag "picard/addorreplacereadgroups" setup { run("BWA_INDEX") { @@ -50,11 +49,11 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]) input[2] = BWA_INDEX.out.index - input[3] = false // skip_deduplication - input[4] = true // use_gpu - input[5] = "bam" // output_fmt - input[6] = Channel.of([[:], []]) // interval_file - input[7] = Channel.of([[:], []]) // known_sites + input[3] = false // skip_deduplication + input[4] = true // use_gpu + input[5] = "bam" // output_fmt + input[6] = Channel.of([[:], []]) // interval_file + input[7] = Channel.of([[:], [], []]) // known_sites """ } } @@ -91,11 +90,11 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]) input[2] = BWA_INDEX.out.index - input[3] = true // skip_deduplication - input[4] = true // use_gpu - input[5] = "bam" // output_fmt - input[6] = Channel.of([[:], []]) // interval_file - input[7] = Channel.of([[:], []]) // known_sites + input[3] = true // skip_deduplication + input[4] = true // use_gpu + input[5] = "bam" // output_fmt + input[6] = Channel.of([[:], []]) // interval_file + input[7] = Channel.of([[:], [], []]) // known_sites """ } } @@ -136,11 +135,11 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]) input[2] = BWA_INDEX.out.index - input[3] = true // skip_deduplication - input[4] = true // use_gpu - input[5] = "bam" // output_fmt - input[6] = Channel.of([[:], []]) // interval_file - input[7] = Channel.of([[:], []]) // known_sites + input[3] = true // skip_deduplication + input[4] = true // use_gpu + input[5] = "bam" // output_fmt + input[6] = Channel.of([[:], []]) // interval_file + input[7] = Channel.of([[:], [], []]) // known_sites """ } } @@ -178,11 +177,11 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]) input[2] = BWA_INDEX.out.index - input[3] = false // skip_deduplication - input[4] = true // use_gpu - input[5] = "bam" // output_fmt - input[6] = Channel.of([[:], []]) // interval_file - input[7] = Channel.of([[:], []]) // known_sites + input[3] = false // skip_deduplication + input[4] = true // use_gpu + input[5] = "bam" // output_fmt + input[6] = Channel.of([[:], []]) // interval_file + input[7] = Channel.of([[:], [], []]) // known_sites """ } } diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test.snap index 9b25a501..58d4fe2c 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test.snap @@ -22,7 +22,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,c74a03de6d290804fd1b1d502eaec964" + "test.stats:md5,4e6f8fe4c0b86e4e8b6610aae5b9f2a4" ] ], null, @@ -39,11 +39,11 @@ ] ], + "timestamp": "2026-10-28T16:30:19.830446478", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.1" - }, - "timestamp": "2026-04-29T09:12:21.203195056" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "Sarscov2 fasta - PE - skip deduplication - with GPU parabricks/fq2bam": { "content": [ @@ -68,7 +68,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,21b91a04b74c3498ebb73d185a2bfc95" + "test.stats:md5,d161dc029a3ae623d663c1d16155d721" ] ], null, @@ -84,11 +84,11 @@ ] ], + "timestamp": "2026-10-28T16:31:34.058857477", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.1" - }, - "timestamp": "2026-04-29T09:18:12.151141742" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "Sarscov2 fasta - SE - skip deduplication - with GPU parabricks/fq2bam": { "content": [ @@ -113,7 +113,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,c74a03de6d290804fd1b1d502eaec964" + "test.stats:md5,4e6f8fe4c0b86e4e8b6610aae5b9f2a4" ] ], null, @@ -129,11 +129,11 @@ ] ], + "timestamp": "2026-10-28T16:30:57.055573041", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.1" - }, - "timestamp": "2026-04-29T09:17:19.66501576" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "Sarscov2 fasta - SE - deduplicate - with GPU parabricks/fq2bam - stub": { "content": [ @@ -187,10 +187,10 @@ ] ], + "timestamp": "2026-03-13T14:33:18.72025", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-13T14:33:18.72025" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test index dcff16f9..b84d8af3 100755 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test @@ -14,13 +14,14 @@ nextflow_workflow { tag "bwa/mem" tag "parabricks/fq2bam" tag "samtools" - tag "samtools/sort" - tag "samtools/index" - tag "samtools/idxstats" tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/index" + tag "samtools/sort" tag "samtools/stats" tag "bam_sort_stats_samtools" tag "fastq_align_bwa" + tag "picard" tag "picard/markduplicates" tag "picard/addorreplacereadgroups" @@ -57,7 +58,7 @@ nextflow_workflow { input[4] = false // use_gpu input[5] = "bam" // output_fmt input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites + input[7] = [[:], [], [] ] // known_sites """ } } @@ -101,7 +102,7 @@ nextflow_workflow { input[4] = false // use_gpu input[5] = "bam" // output_fmt input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites + input[7] = [[:], [], [] ] // known_sites """ } } @@ -145,7 +146,7 @@ nextflow_workflow { input[4] = false // use_gpu input[5] = "bam" // output_fmt input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites + input[7] = [[:], [], [] ] // known_sites """ } } @@ -186,7 +187,7 @@ nextflow_workflow { input[4] = false // use_gpu input[5] = "bam" // output_fmt input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites + input[7] = [[:], [], [] ] // known_sites """ } } diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/nextflow.config index 34fe7e51..b4e0ab29 100755 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/nextflow.config +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/nextflow.config @@ -1,5 +1,6 @@ process { withName: PARABRICKS_FQ2BAM { + ext.args = '' // The nf-test config caps system memory usage to 4.GB // This module requires at least 15 GB to run without error // Note: The Github runners run GPU tests on a machine with 15.1 GB available memory diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf index 9e247330..82bea67c 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf @@ -1,3 +1,6 @@ +// Copyright (c) the nf-core community under an open-source MIT license. +// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing. + include { BWAMETH_ALIGN } from '../../../modules/nf-core/bwameth/align/main' include { PARABRICKS_FQ2BAMMETH } from '../../../modules/nf-core/parabricks/fq2bammeth/main' include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml index 2af9ed18..adf3e0c2 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml @@ -83,12 +83,6 @@ output: Channel containing files for MultiQC input (metrics, stats, flagstat). Structure: [ path(files) ] pattern: "*.{txt,stats,flagstat}" - - versions: - type: file - description: | - File containing software versions - Structure: [ path(versions.yml) ] - pattern: "versions.yml" authors: - "@sateeshperi" maintainers: diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test index d522d6e8..5fea79a7 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test @@ -6,17 +6,21 @@ nextflow_workflow { config "./nextflow.config" tag "gpu" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_align_dedup_bwameth" + tag "bwameth" tag "bwameth/align" + tag "parabricks" tag "parabricks/fq2bammeth" - tag "samtools/sort" - tag "samtools/index" - tag "samtools/flagstat" - tag "samtools/stats" + tag "picard" tag "picard/markduplicates" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/index" tag "samtools/index" + tag "samtools/sort" + tag "samtools/stats" + tag "subworkflows" + tag "subworkflows/fastq_align_dedup_bwameth" + tag "subworkflows_nfcore" tag "untar" setup { diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap index 5b5e9f40..0c423fc5 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap @@ -22,7 +22,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,8e2d01b60192eaa8abe0e2fcb1aded96" + "test.stats:md5,6b2f6b7f0760aa765a8b64d1bba968f4" ] ], [ @@ -34,11 +34,11 @@ "test.stats" ] ], + "timestamp": "2026-10-28T16:24:13.178363664", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-04-30T11:11:35.981680654" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "Params: parabricks/fq2bammeth single-end | use_gpu | skip_deduplication": { "content": [ @@ -63,7 +63,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,8e2d01b60192eaa8abe0e2fcb1aded96" + "test.stats:md5,6b2f6b7f0760aa765a8b64d1bba968f4" ] ], [ @@ -74,10 +74,10 @@ "test.stats" ] ], + "timestamp": "2026-10-28T16:24:51.315253302", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-04-30T11:12:28.491332509" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test index d4343716..253d35e1 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test @@ -5,17 +5,20 @@ nextflow_workflow { workflow "FASTQ_ALIGN_DEDUP_BWAMETH" config "./nextflow.config" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_align_dedup_bwameth" + tag "bwameth" tag "bwameth/align" + tag "parabricks" tag "parabricks/fq2bammeth" - tag "samtools/sort" - tag "samtools/index" - tag "samtools/flagstat" - tag "samtools/stats" tag "picard/markduplicates" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/index" tag "samtools/index" + tag "samtools/sort" + tag "samtools/stats" + tag "subworkflows" + tag "subworkflows/fastq_align_dedup_bwameth" + tag "subworkflows_nfcore" tag "untar" setup { diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap index 758d7f38..a6755c98 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,8e2d01b60192eaa8abe0e2fcb1aded96" + "test.stats:md5,6b2f6b7f0760aa765a8b64d1bba968f4" ] ], [ @@ -34,10 +34,10 @@ "test.stats" ] ], - "timestamp": "2026-03-12T14:02:51.192166217", + "timestamp": "2026-10-28T07:54:02.823554", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.10.4" } }, "Params: bwameth paired-end | skip_deduplication": { @@ -63,7 +63,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,193e7eea4f35311c222d8346a8863eb9" + "test.stats:md5,43014e45d5e8fec6020fba559916241b" ] ], [ @@ -74,10 +74,10 @@ "test.stats" ] ], - "timestamp": "2026-03-12T14:03:21.524028875", + "timestamp": "2026-10-28T07:54:57.116114", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.10.4" } }, "Params: bwameth paired-end | default": { @@ -103,7 +103,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,193e7eea4f35311c222d8346a8863eb9" + "test.stats:md5,43014e45d5e8fec6020fba559916241b" ] ], [ @@ -115,10 +115,10 @@ "test.stats" ] ], - "timestamp": "2026-03-12T14:03:09.246819707", + "timestamp": "2026-10-28T07:54:40.489171", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.10.4" } } -} +} \ No newline at end of file diff --git a/tests/.nftignore b/tests/.nftignore index 6539b02e..2be540b0 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -23,6 +23,7 @@ multiqc/*/multiqc_data/multiqc_software_versions.txt multiqc/*/multiqc_data/multiqc_sources.txt multiqc/*/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg} multiqc/*/multiqc_report.html +parabricks/*.{bam,bam.bai} pipeline_info/*.{html,json,txt,yml} qualimap/**/images_qualimapReport/* qualimap/**/raw_data_qualimapReport/* diff --git a/tests/bismark_hisat_variants.nf.test.snap b/tests/bismark_hisat_variants.nf.test.snap index 064f6b51..3bd86604 100644 --- a/tests/bismark_hisat_variants.nf.test.snap +++ b/tests/bismark_hisat_variants.nf.test.snap @@ -27,10 +27,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -291,10 +291,10 @@ ] ] ], - "timestamp": "2026-07-20T19:16:41.508363954", + "timestamp": "2026-11-11T20:27:32.005208386", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark_hisat with save_reference and save_align_intermeds": { @@ -328,10 +328,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -643,10 +643,10 @@ ] ] ], - "timestamp": "2026-07-20T19:17:19.329231913", + "timestamp": "2026-11-11T20:28:25.878822611", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark_hisat": { @@ -680,10 +680,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -934,10 +934,10 @@ ] ] ], - "timestamp": "2026-07-20T19:16:06.36468586", + "timestamp": "2026-11-11T20:26:40.593986768", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/bismark_variants.nf.test.snap b/tests/bismark_variants.nf.test.snap index ed1b88eb..c65b0a17 100644 --- a/tests/bismark_variants.nf.test.snap +++ b/tests/bismark_variants.nf.test.snap @@ -33,10 +33,10 @@ "qualimap": 2.3 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -525,10 +525,10 @@ ] ] ], - "timestamp": "2026-07-20T19:36:26.316225986", + "timestamp": "2026-11-11T20:35:43.890101586", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with nomeseq": { @@ -565,10 +565,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -863,10 +863,10 @@ ] ] ], - "timestamp": "2026-07-20T19:34:22.697526855", + "timestamp": "2026-11-11T20:31:36.521994093", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with skip_multiqc": { @@ -897,10 +897,10 @@ "gunzip": 1.13 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1081,10 +1081,10 @@ ] ] ], - "timestamp": "2026-07-20T19:36:57.42305155", + "timestamp": "2026-11-11T20:36:19.338788912", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark (default)": { @@ -1118,10 +1118,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1372,10 +1372,10 @@ ] ] ], - "timestamp": "2026-07-20T19:30:38.256291297", + "timestamp": "2026-11-11T20:26:17.050165941", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with cytosine_report": { @@ -1412,10 +1412,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1686,10 +1686,10 @@ ] ] ], - "timestamp": "2026-07-20T19:32:29.192431742", + "timestamp": "2026-11-11T20:28:49.715065505", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with em_seq and clip_r1": { @@ -1723,10 +1723,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1977,10 +1977,10 @@ ] ] ], - "timestamp": "2026-07-20T19:33:43.410840251", + "timestamp": "2026-11-11T20:30:44.682019861", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with skip_trimming": { @@ -2014,10 +2014,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "Workflow": { "nf-core/methylseq": "v4.3.0dev" @@ -2238,10 +2238,10 @@ ] ] ], - "timestamp": "2026-07-19T18:28:06.288141981", + "timestamp": "2026-11-11T20:26:59.858632562", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with skip_deduplication": { @@ -2272,10 +2272,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -2536,10 +2536,10 @@ ] ] ], - "timestamp": "2026-07-20T19:31:50.167091073", + "timestamp": "2026-11-11T20:27:52.46214294", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with rrbs": { @@ -2570,10 +2570,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -2834,10 +2834,10 @@ ] ] ], - "timestamp": "2026-07-20T19:33:05.71017654", + "timestamp": "2026-11-11T20:29:49.152121411", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with save_reference and save_align_intermeds": { @@ -2871,10 +2871,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -3180,10 +3180,10 @@ ] ] ], - "timestamp": "2026-07-20T19:35:00.690480363", + "timestamp": "2026-11-11T20:32:24.994270622", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with run_methurator": { @@ -3223,10 +3223,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -3504,10 +3504,10 @@ "8a3399c0ab4dcb2505bdf272b987da1a" ] ], - "timestamp": "2026-07-22T15:01:07.458183", + "timestamp": "2026-11-11T20:34:52.019527503", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.0" + "nextflow": "25.10.4" } }, "Params: bismark with CAT_FASTQ and skip_trimming and skip_deduplication": { @@ -3541,10 +3541,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "Workflow": { "nf-core/methylseq": "v4.3.0dev" @@ -3708,10 +3708,10 @@ ] ] ], - "timestamp": "2026-07-19T18:34:49.494410127", + "timestamp": "2026-11-11T20:38:05.062620944", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with run_preseq": { @@ -3745,13 +3745,13 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT_PRESEQ": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -4002,9 +4002,9 @@ ] ] ], - "timestamp": "2026-10-26T10:05:14.742765", + "timestamp": "2026-11-11T20:33:20.325041263", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -4036,10 +4036,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -4255,10 +4255,10 @@ ] ] ], - "timestamp": "2026-07-20T19:37:33.610087109", + "timestamp": "2026-11-11T20:37:19.821800307", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/bwamem3_bisulfite.nf.test.snap b/tests/bwamem3_bisulfite.nf.test.snap index be54eb94..d6f69be8 100644 --- a/tests/bwamem3_bisulfite.nf.test.snap +++ b/tests/bwamem3_bisulfite.nf.test.snap @@ -24,19 +24,19 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -185,16 +185,16 @@ [ "Ecoli_10K_methylated.flagstat:md5,f863974bec4cf02dbf1d8bc543b7e885", "Ecoli_10K_methylated.idxstats:md5,5434a7d7629d6d1da4c1cfff94added8", - "Ecoli_10K_methylated.stats:md5,f9dc158e8808e0141513339923396d63", + "Ecoli_10K_methylated.stats:md5,035eb0cbacc26a66c5e68b293bfead02", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", "SRR389222_sub1.idxstats:md5,a76229d666e06745c425b1d4614a5e0a", - "SRR389222_sub1.stats:md5,126d325a2a510b6860315da5ce862b8e", + "SRR389222_sub1.stats:md5,4f841766d68db324837489516beffa1c", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", "SRR389222_sub2.idxstats:md5,ebe2aa0dee55a2cca168e4ffb321bd98", - "SRR389222_sub2.stats:md5,abc210ca6d917df4b25b0486632cac1a", + "SRR389222_sub2.stats:md5,070151866af801dcd6c43dcfd1301466", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", "SRR389222_sub3.idxstats:md5,1356141cf13f06c83527233a122fe1bd", - "SRR389222_sub3.stats:md5,72bd859bbf46519b434cdfc3c5f3cf58", + "SRR389222_sub3.stats:md5,6eeab3abcf99776289563832dd80e094", "genome.fa.amb:md5,c5a18088a0c677c9cdcebec36f2cf418", "genome.fa.ann:md5,78b2fd32c283fbf8ba7624b883349a57", "genome.fa.bwt.2bit.64:md5,fd4cafe48f3ed26cd602494df58fe02e", @@ -279,7 +279,7 @@ ] ] ], - "timestamp": "2026-11-10T19:56:12.465014538", + "timestamp": "2026-11-11T20:29:18.581935278", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -310,19 +310,19 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -453,16 +453,16 @@ [ "Ecoli_10K_methylated.flagstat:md5,f863974bec4cf02dbf1d8bc543b7e885", "Ecoli_10K_methylated.idxstats:md5,5434a7d7629d6d1da4c1cfff94added8", - "Ecoli_10K_methylated.stats:md5,f9dc158e8808e0141513339923396d63", + "Ecoli_10K_methylated.stats:md5,035eb0cbacc26a66c5e68b293bfead02", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", "SRR389222_sub1.idxstats:md5,a76229d666e06745c425b1d4614a5e0a", - "SRR389222_sub1.stats:md5,126d325a2a510b6860315da5ce862b8e", + "SRR389222_sub1.stats:md5,4f841766d68db324837489516beffa1c", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", "SRR389222_sub2.idxstats:md5,ebe2aa0dee55a2cca168e4ffb321bd98", - "SRR389222_sub2.stats:md5,abc210ca6d917df4b25b0486632cac1a", + "SRR389222_sub2.stats:md5,070151866af801dcd6c43dcfd1301466", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", "SRR389222_sub3.idxstats:md5,1356141cf13f06c83527233a122fe1bd", - "SRR389222_sub3.stats:md5,72bd859bbf46519b434cdfc3c5f3cf58", + "SRR389222_sub3.stats:md5,6eeab3abcf99776289563832dd80e094", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3d0166e240945cce69e493945e7501b", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -523,7 +523,7 @@ ] ] ], - "timestamp": "2026-11-10T19:55:38.66175238", + "timestamp": "2026-11-11T20:27:30.907963193", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -554,13 +554,13 @@ "multiqc": 1.34 }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -679,16 +679,16 @@ [ "Ecoli_10K_methylated.flagstat:md5,f863974bec4cf02dbf1d8bc543b7e885", "Ecoli_10K_methylated.idxstats:md5,5434a7d7629d6d1da4c1cfff94added8", - "Ecoli_10K_methylated.stats:md5,6b8d944377d38f418869d9347d93c298", + "Ecoli_10K_methylated.stats:md5,6ab8ef3f2e57b82b51ec0d3ac309b8a5", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", "SRR389222_sub1.idxstats:md5,a76229d666e06745c425b1d4614a5e0a", - "SRR389222_sub1.stats:md5,fe4631170b2284cd3cfc056fb7eb2a1a", + "SRR389222_sub1.stats:md5,a8d9919098f1eb132062b8bfc25c749e", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", "SRR389222_sub2.idxstats:md5,ebe2aa0dee55a2cca168e4ffb321bd98", - "SRR389222_sub2.stats:md5,7e167ca85f23dccbd4e879da2ec5513e", + "SRR389222_sub2.stats:md5,f0190527941dc28f1d2e932c1ba5eb1e", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", "SRR389222_sub3.idxstats:md5,1356141cf13f06c83527233a122fe1bd", - "SRR389222_sub3.stats:md5,27c11ef0e956c0f0c1fe52f50d1527db", + "SRR389222_sub3.stats:md5,187d51d95fbdf3b1c2210ef9202738ff", "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,6b4241683a6a924959cd00370a0f4e47", "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", @@ -743,7 +743,7 @@ ] ] ], - "timestamp": "2026-11-10T19:55:53.792663273", + "timestamp": "2026-11-11T20:28:20.529257579", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/bwamem3_taps.nf.test.snap b/tests/bwamem3_taps.nf.test.snap index bc4a55dd..e5a63a2f 100644 --- a/tests/bwamem3_taps.nf.test.snap +++ b/tests/bwamem3_taps.nf.test.snap @@ -18,7 +18,7 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "RASTAIR_CALL": { "rastair": "0.8.2" @@ -33,16 +33,16 @@ "rastair": "0.8.2" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -155,10 +155,10 @@ [ "taps_pe.flagstat:md5,de46769ec7a98e0c36956360e7004ee3", "taps_pe.idxstats:md5,9f883ed7b159eac3517153a4c2175486", - "taps_pe.stats:md5,8a49f392fe30a95791c844fdcefb7fee", + "taps_pe.stats:md5,23668adadf25517fd30c2bb78e3d0acb", "taps_se.flagstat:md5,3224dc14d5a1c0868dcccdfebc4c41ab", "taps_se.idxstats:md5,32d1a6e2511cb7bfcad6f1759588e4c7", - "taps_se.stats:md5,ec3871038ce25fc4eb18c5b7b213e46d", + "taps_se.stats:md5,94c005937e69c43fa5a42eeddc85aa22", "cutadapt_filtered_reads_plot.txt:md5,b236966103084cc68b0880ac5afc9f3a", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,7dc9dedceec6b1632be5af9fdd450e90", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,4de0b352da2ca07b3b768707e45a0551", @@ -208,7 +208,7 @@ ] ] ], - "timestamp": "2026-11-10T19:43:23.011441159", + "timestamp": "2026-11-11T20:31:56.313359659", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -249,7 +249,7 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "RASTAIR2_CALL": { "tabix": 1.24 @@ -258,16 +258,16 @@ "rastair": "2.2.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -392,10 +392,10 @@ [ "taps_pe.flagstat:md5,de46769ec7a98e0c36956360e7004ee3", "taps_pe.idxstats:md5,9f883ed7b159eac3517153a4c2175486", - "taps_pe.stats:md5,8a49f392fe30a95791c844fdcefb7fee", + "taps_pe.stats:md5,23668adadf25517fd30c2bb78e3d0acb", "taps_se.flagstat:md5,3224dc14d5a1c0868dcccdfebc4c41ab", "taps_se.idxstats:md5,32d1a6e2511cb7bfcad6f1759588e4c7", - "taps_se.stats:md5,ec3871038ce25fc4eb18c5b7b213e46d", + "taps_se.stats:md5,94c005937e69c43fa5a42eeddc85aa22", "bcftools-stats-subtypes.txt:md5,29578ebf9f5d30a4649d223775fb798a", "bcftools_stats_indel-lengths.txt:md5,520280af2576dcfa9afe6a2f27385021", "bcftools_stats_variant_depths.txt:md5,1fa7e471d1eddf8bf92fb5efce56699a", @@ -462,7 +462,7 @@ ] ] ], - "timestamp": "2026-11-10T19:58:23.640015454", + "timestamp": "2026-11-11T20:34:42.53069354", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/bwamem_taps.nf.test.snap b/tests/bwamem_taps.nf.test.snap index 256fb707..e71daaab 100644 --- a/tests/bwamem_taps.nf.test.snap +++ b/tests/bwamem_taps.nf.test.snap @@ -18,10 +18,10 @@ "multiqc": 1.34 }, "PICARD_ADDORREPLACEREADGROUPS": { - "picard": "3.4.0" + "picard": "3.5.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "RASTAIR_CALL": { "rastair": "0.8.2" @@ -36,19 +36,19 @@ "rastair": "0.8.2" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -179,16 +179,16 @@ [ "Ecoli_10K_methylated.flagstat:md5,6875b2d49eec4f8b199bceda4f3ab148", "Ecoli_10K_methylated.idxstats:md5,bfccbb1237079763a8b6625821423ed0", - "Ecoli_10K_methylated.stats:md5,965d7d335a6f918ee8ec6d359afc5651", + "Ecoli_10K_methylated.stats:md5,00b55f69c32c2c1afc1911a4e6ae2e4a", "SRR389222_sub1.flagstat:md5,fbfec3e5592cbb11f050ed06983f2bbd", "SRR389222_sub1.idxstats:md5,47eaa730cb2000975476b03df209a5e8", - "SRR389222_sub1.stats:md5,78965287ea508ee7b387cf9614de7de2", + "SRR389222_sub1.stats:md5,89728688d02814ac39e85cff780f461b", "SRR389222_sub2.flagstat:md5,0ad57bb4ef7b258fc23d9b3ab7ed26b4", "SRR389222_sub2.idxstats:md5,766288f18a1767e4b95c7383005161e8", - "SRR389222_sub2.stats:md5,3622a00daee1b2dbe01fcabb6f130c01", + "SRR389222_sub2.stats:md5,6396ea3639b211ccf5c8e04703bb394e", "SRR389222_sub3.flagstat:md5,c6e3f93f66e47ff2138f640eaebd1c3b", "SRR389222_sub3.idxstats:md5,59fa8ca802e25072377a7527a6801f9b", - "SRR389222_sub3.stats:md5,8c80eeb3baf1fcbaf02cbdff40ab22ae", + "SRR389222_sub3.stats:md5,cd89c2e299fbb90071a07c47cbfc4c95", "cutadapt_filtered_reads_plot.txt:md5,ff1b6d4011a5be5410b9404f7ff56c56", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,57d07c19b0c30dc88df96c30bedcdc33", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,1e5ca4193f8290c5c812334d03615b41", @@ -247,7 +247,7 @@ ] ] ], - "timestamp": "2026-11-10T19:44:10.107977004", + "timestamp": "2026-11-11T20:38:54.532483689", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/bwamem_taps_use_gpu.nf.test b/tests/bwamem_taps_use_gpu.nf.test new file mode 100644 index 00000000..159c79ab --- /dev/null +++ b/tests/bwamem_taps_use_gpu.nf.test @@ -0,0 +1,33 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - BWA-MEM with TAPS GPU" + script "../main.nf" + config "./nextflow.config" + tag "gpu" + + test("Params: PARABRICKS_FQ2BAM - bwamem | taps - GPU Profile") { + when { + params { + aligner = "bwamem" + taps = true + outdir = "$outputDir" + } + } + + then { + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'multiqc/*/multiqc_plots', 'multiqc/*/multiqc_plots/**', '**/multiqc.parquet']) + def stable_path = getAllFilesFromDir(params.outdir, ignore: ['**/multiqc.parquet'], ignoreFile: 'tests/.nftignore') + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + stable_name, + stable_path, + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwamem_taps_use_gpu.nf.test.snap b/tests/bwamem_taps_use_gpu.nf.test.snap new file mode 100644 index 00000000..854a00fa --- /dev/null +++ b/tests/bwamem_taps_use_gpu.nf.test.snap @@ -0,0 +1,305 @@ +{ + "Params: PARABRICKS_FQ2BAM - bwamem | taps - GPU Profile": { + "content": [ + { + "BWA_INDEX": { + "bwa": "0.7.19-r1273" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.13 + }, + "MULTIQC": { + "multiqc": 1.34 + }, + "PARABRICKS_FQ2BAM": { + "parabricks": "4.8.0-1" + }, + "PICARD_ADDORREPLACEREADGROUPS": { + "picard": "3.5.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.5.0" + }, + "RASTAIR_CALL": { + "rastair": "0.8.2" + }, + "RASTAIR_MBIAS": { + "rastair": "0.8.2" + }, + "RASTAIR_MBIASPARSER": { + "rastair": "0.8.2" + }, + "RASTAIR_METHYLKIT": { + "rastair": "0.8.2" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.25 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.25 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.25 + }, + "SAMTOOLS_SORT": { + "samtools": 1.25 + }, + "SAMTOOLS_STATS": { + "samtools": 1.25 + }, + "TRIMGALORE": { + "trimgalore": "2.3.0" + }, + "Workflow": { + "nf-core/methylseq": "v4.3.0dev" + } + }, + [ + "bwamem", + "bwamem/alignments", + "bwamem/alignments/samtools_stats", + "bwamem/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", + "bwamem/alignments/samtools_stats/Ecoli_10K_methylated.idxstats", + "bwamem/alignments/samtools_stats/Ecoli_10K_methylated.stats", + "bwamem/alignments/samtools_stats/SRR389222_sub1.flagstat", + "bwamem/alignments/samtools_stats/SRR389222_sub1.idxstats", + "bwamem/alignments/samtools_stats/SRR389222_sub1.stats", + "bwamem/alignments/samtools_stats/SRR389222_sub2.flagstat", + "bwamem/alignments/samtools_stats/SRR389222_sub2.idxstats", + "bwamem/alignments/samtools_stats/SRR389222_sub2.stats", + "bwamem/alignments/samtools_stats/SRR389222_sub3.flagstat", + "bwamem/alignments/samtools_stats/SRR389222_sub3.idxstats", + "bwamem/alignments/samtools_stats/SRR389222_sub3.stats", + "bwamem/deduplicated", + "bwamem/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", + "bwamem/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwamem/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub1.markdup.sorted.bam", + "bwamem/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub2.markdup.sorted.bam", + "bwamem/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub3.markdup.sorted.bam", + "bwamem/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub3.sorted.bam.bai", + "bwamem/deduplicated/picard_metrics", + "bwamem/deduplicated/picard_metrics/Ecoli_10K_methylated.markdup.sorted.metrics.txt", + "bwamem/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.metrics.txt", + "bwamem/deduplicated/picard_metrics/SRR389222_sub2.markdup.sorted.metrics.txt", + "bwamem/deduplicated/picard_metrics/SRR389222_sub3.markdup.sorted.metrics.txt", + "fastqc", + "fastqc/Ecoli_10K_methylated_1_fastqc.html", + "fastqc/Ecoli_10K_methylated_2_fastqc.html", + "fastqc/SRR389222_sub1_fastqc.html", + "fastqc/SRR389222_sub2_fastqc.html", + "fastqc/SRR389222_sub3_fastqc.html", + "fastqc/zips", + "fastqc/zips/Ecoli_10K_methylated_1_fastqc.zip", + 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"2026-11-11T13:44:52.325000" } } diff --git a/tests/bwameth_variants.nf.test.snap b/tests/bwameth_variants.nf.test.snap index 9e9193ca..0acaad8e 100644 --- a/tests/bwameth_variants.nf.test.snap +++ b/tests/bwameth_variants.nf.test.snap @@ -24,25 +24,25 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "QUALIMAP_BAMQC": { "qualimap": 2.3 }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -310,13 +310,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,6974c6a6bd7478005791f21c7f05d7a0", + 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"SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,27c11ef0e956c0f0c1fe52f50d1527db", + "SRR389222_sub3.stats:md5,187d51d95fbdf3b1c2210ef9202738ff", "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,aa88f19284e63097e9abccac4d7c6669", "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", @@ -600,7 +600,7 @@ ] ] ], - "timestamp": "2026-11-10T00:50:13.776524534", + "timestamp": "2026-11-11T20:32:15.053467895", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -628,22 +628,22 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, 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"SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -1175,7 +1175,7 @@ ] ] ], - "timestamp": "2026-11-10T00:48:04.852388408", + "timestamp": "2026-11-11T20:29:28.366273274", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1203,22 +1203,22 @@ "methyldackel": "0.6.1" }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1300,13 +1300,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,6974c6a6bd7478005791f21c7f05d7a0", + 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"2026-11-11T20:37:10.158951261", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1366,22 +1366,22 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "Workflow": { "nf-core/methylseq": "v4.3.0dev" @@ -1477,13 +1477,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", - "Ecoli_10K_methylated.stats:md5,df3dc85a83ad7e7cc07a91d6742da67a", + "Ecoli_10K_methylated.stats:md5,6394a473b9421b4c49d7bdf54f2920cb", "SRR389222_sub1.flagstat:md5,897d500a710a56a7098172167fa71108", - "SRR389222_sub1.stats:md5,c5d493eed10203dafc1baf78a953610e", + "SRR389222_sub1.stats:md5,0c4fbb74ac42d6ce7524773749826936", "SRR389222_sub2.flagstat:md5,37d33d68b31d4550620dc17582a3a750", - "SRR389222_sub2.stats:md5,d0fa689a679284057dd1bd073ddf62f3", + "SRR389222_sub2.stats:md5,963ea51282b8299693268fe813cba7f1", "SRR389222_sub3.flagstat:md5,e3e925a7b7356e93d14f5e9e102c55b7", - "SRR389222_sub3.stats:md5,e9dae75b994ea52f0ef5fb86e4e40b08", + "SRR389222_sub3.stats:md5,2a93da9f4eb11b0f33c1bb953e9ee11d", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,b43c4c8ff346ae865b2b5db996650942", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -1536,7 +1536,7 @@ ] ] ], - "timestamp": "2026-11-10T00:49:33.699964332", + "timestamp": "2026-11-11T20:31:13.889235355", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1567,22 +1567,22 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, 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"SRR389222_sub2.stats:md5,f0190527941dc28f1d2e932c1ba5eb1e", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,27c11ef0e956c0f0c1fe52f50d1527db", + "SRR389222_sub3.stats:md5,187d51d95fbdf3b1c2210ef9202738ff", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -1767,7 +1767,7 @@ ] ] ], - "timestamp": "2026-11-10T00:48:49.476979667", + "timestamp": "2026-11-11T20:30:22.473443187", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1798,22 +1798,22 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1955,13 +1955,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,6974c6a6bd7478005791f21c7f05d7a0", + "Ecoli_10K_methylated.stats:md5,4471df18edeef3b773bb3dcdabbbb447", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,fe4631170b2284cd3cfc056fb7eb2a1a", + "SRR389222_sub1.stats:md5,a8d9919098f1eb132062b8bfc25c749e", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,7e167ca85f23dccbd4e879da2ec5513e", + "SRR389222_sub2.stats:md5,f0190527941dc28f1d2e932c1ba5eb1e", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,27c11ef0e956c0f0c1fe52f50d1527db", + "SRR389222_sub3.stats:md5,187d51d95fbdf3b1c2210ef9202738ff", "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", @@ -2056,7 +2056,7 @@ ] ] ], - "timestamp": "2026-11-10T00:51:40.177254782", + "timestamp": "2026-11-11T20:34:09.709457217", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -2087,16 +2087,16 @@ "multiqc": 1.34 }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -2206,13 +2206,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,c6a9a8b50c5e1d239071a8b75bc63b4f", - "Ecoli_10K_methylated.stats:md5,b99f4dcb8229f13f6044a16b70ce7d9e", + "Ecoli_10K_methylated.stats:md5,7cd873d9adf4407a13908bb78aec9fcb", "SRR389222_sub1.flagstat:md5,cccae088e2f8686b890d019b60f63065", - "SRR389222_sub1.stats:md5,159ac39b4f3367c783d92c9cdce7d38d", + "SRR389222_sub1.stats:md5,c42c3588a115259a3fc0603f4021c772", "SRR389222_sub2.flagstat:md5,403af1bed1e3e96f5e04d65e96728828", - "SRR389222_sub2.stats:md5,2456a2a40283e80afdc88965c20bacda", + "SRR389222_sub2.stats:md5,3ed5c75e638804d5d4b7ca069f0d31dc", "SRR389222_sub3.flagstat:md5,73a5cb246f6388d5d449775d6e35f5fa", - "SRR389222_sub3.stats:md5,e0cbcb11525b99e9d2b0962e81595564", + "SRR389222_sub3.stats:md5,c4b7828ac5e8cb5a29ea9f4ad65c98af", "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,5e0bf8c8bb3162de75203784414a6399", "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", @@ -2263,7 +2263,7 @@ ] ] ], - "timestamp": "2026-11-10T00:50:53.867680086", + "timestamp": "2026-11-11T20:33:13.736450005", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/combined_index.nf.test.snap b/tests/combined_index.nf.test.snap index 61d6c969..a56ace90 100644 --- a/tests/combined_index.nf.test.snap +++ b/tests/combined_index.nf.test.snap @@ -30,10 +30,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -364,10 +364,10 @@ ] ] ], - "timestamp": "2026-07-20T23:14:35.661338567", + "timestamp": "2026-11-11T20:28:51.617764451", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with combined_index and pbat": { @@ -401,10 +401,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -705,10 +705,10 @@ ] ] ], - "timestamp": "2026-07-20T23:15:13.58145008", + "timestamp": "2026-11-11T20:29:49.86998655", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with combined_index (directional)": { @@ -742,10 +742,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1046,10 +1046,10 @@ ] ] ], - "timestamp": "2026-07-20T23:13:58.485872407", + "timestamp": "2026-11-11T20:27:53.965117386", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark_hisat with combined_index (directional)": { @@ -1083,10 +1083,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1396,10 +1396,10 @@ ] ] ], - "timestamp": "2026-07-20T23:15:49.827068248", + "timestamp": "2026-11-11T20:30:44.204628475", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index fa3b9849..ea800423 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -30,10 +30,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -284,10 +284,10 @@ ] ] ], - "timestamp": "2026-07-20T19:11:36.835039051", + "timestamp": "2026-11-11T20:39:09.092644026", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/index_downloads.nf.test.snap b/tests/index_downloads.nf.test.snap index d98a50b2..5d88ace1 100644 --- a/tests/index_downloads.nf.test.snap +++ b/tests/index_downloads.nf.test.snap @@ -27,10 +27,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -43,10 +43,10 @@ } } ], - "timestamp": "2026-07-20T19:12:51.939144355", + "timestamp": "2026-11-11T20:32:07.957401335", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.0" + "nextflow": "25.10.4" } }, "Params: bwamem3 with bwamem3-index": { @@ -71,19 +71,19 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -96,7 +96,7 @@ } } ], - "timestamp": "2026-11-10T20:04:40.450496364", + "timestamp": "2026-11-11T20:36:11.423353252", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -133,10 +133,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -146,10 +146,10 @@ } } ], - "timestamp": "2026-07-22T15:21:39.90353", + "timestamp": "2026-11-11T20:37:02.097690546", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.0" + "nextflow": "25.10.4" } }, "Params: bismark with run_preseq with bowtie2-index": { @@ -180,13 +180,13 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT_PRESEQ": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -199,9 +199,9 @@ } } ], - "timestamp": "2026-10-26T10:06:07.321179", + "timestamp": "2026-11-11T20:32:55.891959978", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -227,22 +227,22 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -255,10 +255,10 @@ } } ], - "timestamp": "2026-07-20T19:14:49.256172434", + "timestamp": "2026-11-11T20:35:16.174392504", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with run_methurator with bowtie2-index": { @@ -295,10 +295,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -311,10 +311,10 @@ } } ], - "timestamp": "2026-07-22T14:49:08.685976", + "timestamp": "2026-11-11T20:34:09.84246957", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.0" + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/tests/targeted_sequencing_variants.nf.test.snap b/tests/targeted_sequencing_variants.nf.test.snap index 53f5d522..0b15ce13 100644 --- a/tests/targeted_sequencing_variants.nf.test.snap +++ b/tests/targeted_sequencing_variants.nf.test.snap @@ -27,22 +27,22 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -168,13 +168,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,6974c6a6bd7478005791f21c7f05d7a0", + "Ecoli_10K_methylated.stats:md5,4471df18edeef3b773bb3dcdabbbb447", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,fe4631170b2284cd3cfc056fb7eb2a1a", + "SRR389222_sub1.stats:md5,a8d9919098f1eb132062b8bfc25c749e", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,7e167ca85f23dccbd4e879da2ec5513e", + "SRR389222_sub2.stats:md5,f0190527941dc28f1d2e932c1ba5eb1e", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,27c11ef0e956c0f0c1fe52f50d1527db", + "SRR389222_sub3.stats:md5,187d51d95fbdf3b1c2210ef9202738ff", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "Ecoli_10K_methylated.markdup.sorted_CpG.targeted.bedGraph:md5,1f3b38af3cf3c2cdf82fe38bb06ae547", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", @@ -235,7 +235,7 @@ ] ] ], - "timestamp": "2026-11-10T00:55:48.04581174", + "timestamp": "2026-11-11T20:39:03.077089601", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -284,10 +284,10 @@ "picard": "3.4.0" }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -556,10 +556,10 @@ ] ] ], - "timestamp": "2026-07-20T19:30:00.164307069", + "timestamp": "2026-11-11T20:41:35.136801712", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bismark with run_targeted_sequencing": { @@ -599,10 +599,10 @@ "multiqc": 1.34 }, "SAMTOOLS_INDEX": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -869,10 +869,10 @@ ] ] ], - "timestamp": "2026-07-20T19:26:39.235852041", + "timestamp": "2026-11-11T20:37:50.150255224", "meta": { "nf-test": "0.9.5", - "nextflow": "25.04.0" + "nextflow": "25.10.4" } }, "Params: bwameth with run_targeted_sequencing and collecthsmetrics": { @@ -909,22 +909,22 @@ "picard": "3.4.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1052,13 +1052,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,6974c6a6bd7478005791f21c7f05d7a0", + "Ecoli_10K_methylated.stats:md5,4471df18edeef3b773bb3dcdabbbb447", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,fe4631170b2284cd3cfc056fb7eb2a1a", + "SRR389222_sub1.stats:md5,a8d9919098f1eb132062b8bfc25c749e", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,7e167ca85f23dccbd4e879da2ec5513e", + "SRR389222_sub2.stats:md5,f0190527941dc28f1d2e932c1ba5eb1e", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,27c11ef0e956c0f0c1fe52f50d1527db", + "SRR389222_sub3.stats:md5,187d51d95fbdf3b1c2210ef9202738ff", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "Ecoli_10K_methylated.markdup.sorted_CpG.targeted.bedGraph:md5,1f3b38af3cf3c2cdf82fe38bb06ae547", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", @@ -1119,7 +1119,7 @@ ] ] ], - "timestamp": "2026-11-10T00:57:25.875764789", + "timestamp": "2026-11-11T20:40:54.415427986", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1153,22 +1153,22 @@ "multiqc": 1.34 }, "PICARD_MARKDUPLICATES": { - "picard": "3.4.0" + "picard": "3.5.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_ALIGNMENTS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_INDEX_DEDUPLICATED": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_SORT": { - "samtools": "1.23.1" + "samtools": 1.25 }, "SAMTOOLS_STATS": { - "samtools": "1.23.1" + "samtools": 1.25 }, "TRIMGALORE": { "trimgalore": "2.3.0" @@ -1310,13 +1310,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,6974c6a6bd7478005791f21c7f05d7a0", + "Ecoli_10K_methylated.stats:md5,4471df18edeef3b773bb3dcdabbbb447", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,fe4631170b2284cd3cfc056fb7eb2a1a", + "SRR389222_sub1.stats:md5,a8d9919098f1eb132062b8bfc25c749e", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,7e167ca85f23dccbd4e879da2ec5513e", + "SRR389222_sub2.stats:md5,f0190527941dc28f1d2e932c1ba5eb1e", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,27c11ef0e956c0f0c1fe52f50d1527db", + "SRR389222_sub3.stats:md5,187d51d95fbdf3b1c2210ef9202738ff", "Ecoli_10K_methylated.markdup.sorted_CHG.bedGraph:md5,9ae25ac4e62f8945e666a41bfc73f085", "Ecoli_10K_methylated.markdup.sorted_CHG.targeted.bedGraph:md5,1c9bd5a4d4c52f82a2a3d5e28bbde7ab", "Ecoli_10K_methylated.markdup.sorted_CHH.bedGraph:md5,1048980ecaaf99cba98f66fcf65cee94", @@ -1393,7 +1393,7 @@ ] ] ], - "timestamp": "2026-11-10T00:56:38.77521518", + "timestamp": "2026-11-11T20:40:04.875933984", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf index 6810f90d..5f26f8a0 100644 --- a/workflows/methylseq/main.nf +++ b/workflows/methylseq/main.nf @@ -195,7 +195,7 @@ workflow METHYLSEQ { workflow.profile.tokenize(',').intersect(['gpu']).size() >= 1, 'bam', [[:], []], - [[:], []], + [[:], [], []], ) ch_bam = FASTQ_ALIGN_DEDUP_BWAMEM.out.bam