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Add Padfoot annotation and ReConPlot figures for the SV/CNA callers - #202
ljwharbers merged 32 commits into
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The whole-genome test has run through, so here is the update promised in the description. Setup: fresh environment on a UCL CS cluster node (Singularity 3.8.5, Nextflow 25.10.7, local executor, work dir on node-local disk which I think is nvme ssd), one paired 40x ONT tumour/normal from raw uBAMs (126 + 113 GB), pipeline defaults with every tool on only Outcome: The two new steps RSS labels were assigned fine: Padfoot 14.2 GB RSS in 1.5 min on Two things not about this PR that may interest you (I may raise them in the SAVANA follow-up issue): |
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Copilot review overview
🟡 Changes recommended
Unresolved critical and moderate findings remain in ReConPlot handling and Padfoot pairing.
Get a fresh assessment by requesting another Copilot review.
Review effort: Lite
Findings: 2
Open (5)
What changed in this PR
Adds default-on Padfoot annotation and ReConPlot visualization for SV/CNA caller pairs, with SAVANA output wiring, containers, parsers, configuration, documentation, and tests.
Changes:
- Adds Padfoot and ReConPlot workflows and modules.
- Extends paired and tumour-only SAVANA outputs.
- Adds R parsers, containers, parameters, documentation, and nf-tests.
Review findings:
- Critical: fix uncompressed VCF handling and preserve ReConPlot pipeline failures.
- Moderate: handle missing SV mates, empty Padfoot inputs, and unconditional downloads.
- Nits: correct changelog placeholders, container documentation, output documentation, and usage admonitions.
| File | Description |
|---|---|
workflows/lrsomatic.nf |
Integrates the new downstream workflows. |
tests/.nftignore |
Ignores generated figures and logs. |
subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf |
Validates new parameters. |
subworkflows/local/tumor_only/tumoronly_savana.nf |
Emits additional SAVANA products. |
subworkflows/local/tests/reconplot_figures.nf.test |
Tests ReConPlot pairing. |
subworkflows/local/tests/padfoot_annotation.nf.test |
Tests Padfoot pairing. |
subworkflows/local/reconplot_figures.nf |
Builds ReConPlot caller-pair inputs. |
subworkflows/local/paired/paired_savana.nf |
Emits additional paired SAVANA products. |
subworkflows/local/padfoot_annotation.nf |
Builds Padfoot inputs and pairing logic. |
README.md |
Documents new outputs and workflow stages. |
nextflow.config |
Adds runtime parameters. |
nextflow_schema.json |
Defines parameter schema entries. |
modules/local/reconplot/tests/nextflow.config |
Configures module tests. |
modules/local/reconplot/tests/main.nf.test.snap |
Stores ReConPlot snapshots. |
modules/local/reconplot/tests/main.nf.test |
Tests ReConPlot I/O. |
modules/local/reconplot/meta.yml |
Documents the module interface. |
modules/local/reconplot/main.nf |
Runs ReConPlot. |
modules/local/reconplot/environment.yml |
Defines R dependencies. |
modules/local/padfoot/tests/nextflow.config |
Configures module tests. |
modules/local/padfoot/tests/main.nf.test.snap |
Stores Padfoot snapshots. |
modules/local/padfoot/tests/main.nf.test |
Tests Padfoot I/O. |
modules/local/padfoot/meta.yml |
Documents the module interface. |
modules/local/padfoot/main.nf |
Runs Padfoot annotation. |
modules/local/padfoot/environment.yml |
Defines Padfoot dependencies. |
docs/usage.md |
Documents parameters and usage. |
docs/output.md |
Documents generated outputs. |
containers/reconplot/README.md |
Documents ReConPlot image builds. |
containers/reconplot/Dockerfile |
Builds the ReConPlot image. |
containers/padfoot/README.md |
Documents Padfoot image builds. |
containers/padfoot/Dockerfile |
Builds the Padfoot image. |
conf/test.config |
Disables unsupported full-genome steps in tests. |
conf/test_full.config |
Disables unsupported full-genome steps in full tests. |
conf/modules.config |
Configures arguments and publishing. |
CITATIONS.md |
Adds tool and dependency citations. |
CHANGELOG.md |
Records the new functionality. |
assets/reconplot/VERSION |
Pins the wrapper revision. |
assets/reconplot/run_reconplot.R |
Provides the plotting CLI. |
assets/reconplot/README.md |
Documents the vendored wrapper. |
assets/reconplot/R/utils_vcf.R |
Provides VCF helpers. |
assets/reconplot/R/utils_common.R |
Provides shared validation utilities. |
assets/reconplot/R/plotting.R |
Renders and saves figures. |
assets/reconplot/R/parsers/wakhan.R |
Parses Wakhan CN output. |
assets/reconplot/R/parsers/severus.R |
Parses Severus SV output. |
assets/reconplot/R/parsers/savana.R |
Parses SAVANA output. |
assets/reconplot/R/parsers/registry.R |
Registers parsers. |
assets/reconplot/R/parsers/lrsomatic.R |
Provides the lrsomatic parser shortcut. |
assets/reconplot/R/parsers/generic.R |
Provides generic table parsing. |
assets/reconplot/R/parsers/ascat.R |
Parses ASCAT CN output. |
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ljwharbers
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Thanks for this. The pairing logic is carefully done. I checked the wiring against dev @ 0cf00bf:
- SEVERUS, ASCAT and WAKHAN use the same meta subMap for paired and tumour-only samples, and SAVANA only joins with itself, so the joins hold.
- A sample missing one side of a pair is dropped rather than failing the run.
pipefailis set, so theRscript | teepipes fail when Rscript fails.- Empty SV sets pass through
validate_sv. - Moving the wiring into subworkflows is the right fix for the JVM's 64 KB method-size limit.
CI is green. Before merge, a few things need attention.
Should fix before merge
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Every default run now needs internet at start-up.
PADFOOT_WGETandRECONPLOT_PKG_WGETdownload about 120 MB from GitHub at run start whenever the steps are enabled, and they are enabled by default. This happens even when no caller pair forms.nf-core pipelines downloaddoes not stage these tarballs, so on compute nodes without internet an upgrade breaks runs for users who never asked for these tools.- The ReConPlot package is already built into the container, so the download is only needed under
-profile conda. Please guard it. - Padfoot already runs in a custom image. Could it be built into that image at the pinned commit? That removes the WGET, and
--padfoot_dirstays for conda and development. It also means runs no longer depend on a personal fork being reachable at run time. - Related question for the maintainers: should
skip_padfoot/skip_reconplotdefault totrueuntil real-data fixtures exist?
- The ReConPlot package is already built into the container, so the download is only needed under
-
docs/output.mdsays ASCAT does not run on tumour-only samples, but it does. Ondev, ASCAT runs on tumour-only samples because ClairS-TO Verdict uses its output (ascat_chmixes inbranched_minimap.tumor_only). Soreconplot/severus_ascat/is produced for tumour-only samples too. That path is not covered by any test: the stub test only gives ASCAT output to pairedsample1. Please fix the sentence and add a tumour-only ASCAT + Severus sample toreconplot_figures.nf.test.
Strongly suggested
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The stub tests count tasks but never check which files were staged. The comments say solution_1's integer VCF and HP BEDs "must be picked", but the assertions only count tasks per sample. A regression that stages solution_2, or the subclonal BEDs, would still pass. One option: have the stubs write their staged inputs, e.g.
ls cn_input sv_input > ${prefix}/staged.txt, and assert on that file. Same forPADFOOT. -
A crash in either step fails the whole run. Both steps inherit
errorStrategy 'finish', so a failure in an optional figure or annotation step at the end of a ~12 h whole-genome run marks the entire run as failed. Two known ways to trigger it:sanitize_regionsstops when--reconplot_regionsnames a contig that has no CN.run_reconplot.Rexits 1 when it writes no files.
Worth a deliberate decision. We have been bitten by blanket
'ignore'hiding failures in CI before, so an explicit warn-and-continue may be the better option. -
The Padfoot genome gate is written twice (see the inline comment).
Nits
containers/reconplot/Dockerfile: a comment still refers to the removedparams.reconplot_url.run_reconplot.R: the help for--baf-tracksays "SAVANA only", but the ASCAT parser supports it and the pipeline passes it for ASCAT.nextflow.config: the comment says "containers ship full Dfam 4.0", but the image has only the root and curated-consensus partitions. The container README is accurate.- CHM13 is a reference we run routinely, and Padfoot skips it with only a warning. A short note in
docs/usage.mdon supplying--padfoot_gff/--padfoot_rmfor CHM13 would help. - Out of scope, but thanks for the numbers:
SAVANA_RUNpeaked at 149 GB againstprocess_high's 72 GB, andSEVERUSat 49.6 GB againstprocess_medium's 36 GB. Worth a separate issue.
| padfoot_src = channel.value([[id: 'padfoot'], file(params.padfoot_dir, type: 'dir', checkIfExists: true)]) | ||
| } | ||
| else { | ||
| PADFOOT_WGET( channel.value([[id: 'padfoot'], params.padfoot_url]) ) |
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This runs on every default run, even when no caller pair forms, and needs GitHub access at start-up. nf-core pipelines download won't stage it. Could Padfoot be built into the (already custom) image at this commit, with --padfoot_dir kept for conda and development?
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Finished, wget is removed and all embedded in the image. One step towards the offline ready, I hope..
| reconplot_pkg = channel.value([[id: 'reconplot_pkg'], file(params.reconplot_pkg_dir, type: 'dir', checkIfExists: true)]) | ||
| } | ||
| else { | ||
| RECONPLOT_PKG_WGET( channel.value([[id: 'reconplot_pkg'], params.reconplot_pkg_url]) ) |
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The container already has ReConPlot installed, so this download is only needed under conda. Suggest guarding it on the conda profile or on !workflow.containerEngine and passing [] otherwise. The module's library(ReConPlot) check already copes with the package being absent.
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Hi Luuk, I’m back! Two quick questions: 1. Regarding the recent PRs (like #196 dropping the conda directive and CI no longer testing for conda), is conda becoming no longer a supported profile for the pipeline as a whole? 2 . am I right to assume lrsomatic is moving toward being fully offline-ready (no run-time downloads under containers)?
Thanks!
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Hi! Yep, we we havent prioritized conda as an option for a while already since one of the earlier tools didn't allow for it. So if a tool doesn't work with conda, don't worry about it. As long as it works with singularity and docker its fine!
Same goes for run-time downloads, ideally we limit this but I do not think it is fully offline-ready, we for example download clair3 models at runtime (although you can specify custom ones).
| └── multiqc | ||
| ``` | ||
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| The `padfoot` and `reconplot` directories are only present when the corresponding step is enabled (`--skip_padfoot`, `--skip_reconplot`); SAVANA's own output lives under `variants/savana`. Within them, each caller-pair subdirectory requires both of its callers to have produced output for that sample: `severus_wakhan` needs `--skip_wakhan false`, `severus_ascat` needs `--skip_ascat false` and a matched normal (ASCAT is not run for tumour-only samples), and the `savana` subdirectories additionally need SAVANA copy number, which is only produced when an SNP source is available (the phased germline VCF for paired samples, or the bundled 1000G panel for tumour-only samples) and SAVANA finds an acceptable purity/ploidy fit. |
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On dev, ASCAT does run on tumour-only samples (Verdict uses its output), so severus_ascat will appear for them too. Please update this sentence and cover that case in the stub test.
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updated, also added the corresponding tests. All passed.
| // | ||
| def padfoot_genome = params.padfoot_genome ?: | ||
| (params.genome == 'GRCh38' ? 'hg38' : params.genome == 'CHM13' ? 'chm13' : null) | ||
| def padfoot_annot_ok = padfoot_genome && ((padfoot_genome in ['hg38', 'mm10']) || (params.padfoot_gff && params.padfoot_rm)) |
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The same logic lives in validateSvAnnotationParams(), with a comment saying the two must mirror each other. Could it be one helper in utils_nfcore_lrsomatic_pipeline that both places call, so they can't drift apart?
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now all sourcing from the utils file
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@claude review |
![claude[bot]](https://avatars.githubusercontent.com/in/1236702?s=60&v=4){kind=small}
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| tag "modules" | ||
| tag "modules_local" | ||
| tag "padfoot" |
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This new module test has no small tag, so PR CI (.github/workflows/nf-test.yml picks tests by small) never runs it. The PR description says these module tests exist and run, but CI skips them. Please add tag "small" like the two subworkflow tests have.
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| tag "modules" | ||
| tag "modules_local" | ||
| tag "reconplot" |
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Same problem as the PADFOOT module test: there is no small tag, so PR CI never runs this test. Please add tag "small".
| // dependencies (guard in `script:`). Built from containers/padfoot/Dockerfile: Padfoot + RepeatMasker 4.2.4 with the | ||
| // Dfam 4.0 root and curated-consensus partitions. Padfoot update = new commit in the Dockerfile, rebuild, re-pin the digest. | ||
| // Override per site with `process { withName: '.*:PADFOOT_(SEVERUS_WAKHAN|SAVANA)' { container = ... } }`. | ||
| container "ghcr.io/tim-yu/padfoot-repeatmasker@sha256:bf134e2ffca5ae5f0b0c85c7f9d189ab0a886c0ba389c5ff7f1d39a39bd58467" |
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This container directive breaks the pipeline convention in REVIEW.md:
- It is one
ghcr.ioreference, without theworkflow.containerEngine == 'singularity' ...ternary used acrossmodules/. - Custom images should be an
oras://docker.io/...-sif/docker.io/...pair. - REVIEW.md asks for Docker Hub, not ghcr, for large Apptainer images. This one bundles RepeatMasker plus the Dfam 4.0 root and curated partitions, so it is large.
As written, Singularity users convert the ghcr Docker image at run time instead of pulling a prebuilt SIF. Please publish to Docker Hub with a matching -sif tag and use the standard ternary. Keep both branches on the same Padfoot commit.
| // No conda: the image ships the ReConPlot R package itself (guard in `script:`); the wrapper is pipeline glue in | ||
| // assets/reconplot/. Built from containers/reconplot/Dockerfile. Package update = new commit there, rebuild, re-pin the digest. | ||
| // Override per site with `process { withName: '.*:RECONPLOT_(SEVERUS_ASCAT|SEVERUS_WAKHAN|SAVANA)' { container = ... } }`. | ||
| container "ghcr.io/tim-yu/reconplot@sha256:1145fc5aebe0227bec371f4c59b08b9a09871498e403c01b83f83973149ae9e7" |
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Same container problem as PADFOOT: this is one ghcr.io reference with no singularity/docker ternary. The pipeline convention for custom images is an oras://docker.io/...-sif / docker.io/... pair on Docker Hub, with both branches on the same ReConPlot commit.
| skip_ascat = true | ||
| skip_modkit = true | ||
| // Padfoot/ReConPlot need whole-genome caller output; covered by the module- and subworkflow-level nf-tests | ||
| skip_padfoot = true |
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With Padfoot and ReConPlot skipped here and in test_full, the only small tests for this feature are -stub runs. So no CI test runs:
- the real
script:blocks of either module; - the ~1,800 lines of R under
assets/reconplot/(parsers for ASCAT, Wakhan, Severus and SAVANA, plotting, region parsing); - Padfoot itself.
A break in the wrapper or in the Padfoot CLI arguments (--specie, --skip_RepeatMasker, --cna-caller savana) would still pass CI. Under REVIEW.md, please run the Slurm test array on real Severus/Wakhan/ASCAT/SAVANA output before merge. Ideally, also add the chr22 fixtures to test-datasets so a non-stub small test can cover at least one pair.
| - `severus_wakhan/` -- Wakhan top-ranked solution CN + Severus somatic SVs | ||
| - `savana/` -- SAVANA absolute CN + SAVANA classified somatic SVs | ||
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| Each pair produces `per_chromosome/` (one figure per chromosome), `genome_wide/` (all chromosomes in one strip), the harmonised CN/SV tables, and, when `--reconplot_regions` is set, a `focus/` multi-panel figure with optional gene labels and BAF track. Both the wrapper and the ReConPlot R package (neither on conda) are staged as source from GitHub (or local checkouts for offline systems); the default container ships the package pre-installed, while `-profile conda` installs it at run time. |
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This sentence contradicts the code and the rest of this section:
- It says the wrapper and the ReConPlot package are "staged as source from GitHub (or local checkouts for offline systems)". In fact the wrapper ships in
assets/reconplot/and the package is inside the image (see line 409 and line 439: "Neither step downloads anything at run time"). - It says "
-profile condainstalls it at run time". In factRECONPLOTraiseserrorunder conda/mamba (modules/local/reconplot/main.nf:31-33).
It looks left over from an earlier design. Please remove it or correct it. The PR description has the same leftovers: --padfoot_dir and "fetch their sources (90 MB + 30 MB) at run start".
| │ │ │ └── samtools | ||
| │ │ └── whatshap_stats | ||
| │ ├── reconplot | ||
| │ │ ├── severus_wakhan |
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This tree is for tumour-only samples, and it leaves out reconplot/severus_ascat. ASCAT runs for tumour-only samples and RECONPLOT_SEVERUS_ASCAT forms for them: the subworkflow test asserts sample3, and line 112 of this file says so. Please add severus_ascat here.
| "description": "Padfoot genome preset (`hg38`, `chm13`, `mm10`). Default: inferred from `--genome`.", | ||
| "help_text": "GRCh38 -> hg38, CHM13 -> chm13. Padfoot bundles gene and repeat annotations for hg38 and mm10 only; chm13 and other presets need `--padfoot_gff` and `--padfoot_rm`, otherwise Padfoot is skipped with a warning." | ||
| }, | ||
| "padfoot_gff": { |
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REVIEW.md asks for a help_text on every new parameter. Only padfoot_genome has one. Some key behaviour is only in docs/usage.md, so it is missing from --help and the nf-core launcher:
padfoot_gffandpadfoot_rmare needed together with a non-hg38/mm10 preset, or Padfoot is skipped.reconplot_regionsis syntax-checked at start-up, and regions on contigs without copy number are skipped.reconplot_baf_trackapplies only to ASCAT and SAVANA.reconplot_genomefalls back to hg38 for custom genomes.
Please add help_text for the other padfoot_* / reconplot_* and skip_padfoot / skip_reconplot params.
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Automated review: 8 inline findings.
The channel joins looked correct to me: Severus, ASCAT, Wakhan and SAVANA all use the same meta subMap, and the joins cannot pair records from different samples. A human reviewer needs to run the real code. All |
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| container "${(workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer') && !task.ext.singularity_pull_docker_container | ||
| ? 'oras://ghcr.io/tim-yu/padfoot-repeatmasker-sif:4.2.4-dfam4-padfoot-e7eaed7' | ||
| : 'ghcr.io/tim-yu/padfoot-repeatmasker:4.2.4-dfam4-padfoot-e7eaed7'}" |
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Container registry does not follow the repo convention. REVIEW.md asks custom images to use the oras://docker.io/...-sif / docker.io/... pair, i.e. Docker Hub rather than ghcr, for large Apptainer images. This image ships RepeatMasker plus the Dfam 4.0 root and curated-consensus partitions, so it is exactly the large Apptainer case that rule is about. modules/local/reconplot/main.nf:8-10 (ghcr.io/tim-yu/reconplot) has the same problem.
The PR description also says both images are "digest-pinned in the module container directives". They are pinned only by mutable tags (4.2.4-dfam4-padfoot-e7eaed7, 0.2-r4.4).
Please push both images to Docker Hub (ideally under the lab org rather than a personal namespace), point these directives at them, and update the description, or pin by @sha256: digest if digest pinning is intended.
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Please let me know if eventually all the images need to be uploaded to Docker hub. I will then upload there.
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We noticed that ghcr hosted images, if they're too big, they very often (unexpectedly) time out, without any good fix on the pipeline side. That's why most of our larger images are hosted on dockerhub now. So ideally, yes, on dockerhub would be better
| // Padfoot/ReConPlot need whole-genome caller output; covered by the module- and subworkflow-level nf-tests | ||
| skip_padfoot = true | ||
| skip_reconplot = true |
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The real script: path of both new modules runs in no CI test. test and test_full skip Padfoot and ReConPlot. Every new small test (both module tests, both subworkflow tests) uses -stub, so CI checks only the channel pairing and file staging.
None of the following ever runs on a PR:
- the Padfoot command line (
--sv-caller/--cna-caller savanafrom the fork,--skip_RepeatMasker,--specie mousefor mm10, the RepeatMasker/Dfam setup in the image); - the three
run_reconplot.Rcalls, including the Wakhanmv cn_input/*.bed cn_input/solution_1/bed_output/re-layout and themv ${prefix}/per_chromosome/*.reconplot_{cn,sv}.tsvstep; - the roughly 2,000 lines of vendored R under
assets/reconplot/.
A break in any of these would still show green CI. Per REVIEW.md, please run the Slurm test array or a whole-genome run with Padfoot and ReConPlot on, and attach the results. Better still, add a small real-data (non-stub) module test once the chr22 fixtures offered in the PR description exist in IntGenomicsLab/test-datasets.
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Working on adding the testing module. And spotted a small bug on Padfoot not correctly annotating some TE event, fixing now.
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Automated review: 2 findings (inline).
A human reviewer needs to check (I cannot run these):
The channel pairing and joins (meta keys, SAVANA remainder join, Wakhan |
…run-time downloads Every default run fetched Padfoot (90 MB, from a personal fork) and the ReConPlot R package (30 MB) from GitHub at start-up, even when no caller pair formed, and `nf-core pipelines download` could not stage them. Following IntGenomicsLab#196: Padfoot is now installed into `ghcr.io/tim-yu/padfoot-repeatmasker` at a pinned, checksum-verified commit (`/opt/padfoot`), the ReConPlot package was already in `ghcr.io/tim-yu/reconplot`, and both modules drop `conda` with the same guard as `LRSOMATICREPORT`. - `PADFOOT_WGET`/`PADFOOT_UNTAR`, `RECONPLOT_PKG_WGET`/`RECONPLOT_PKG_UNTAR` and the params `padfoot_url`, `padfoot_dir`, `reconplot_pkg_url`, `reconplot_pkg_dir` are removed; the module inputs for the staged sources go with them. - The environment.yml files move under `containers/`, where the Dockerfiles use them. - Docs: Padfoot/ReConPlot options, the offline paragraph, a CHM13 note, both container READMEs; the Dfam wording says root + curated-consensus partitions. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…s for tumour-only samples The subworkflow stub tests only counted tasks per sample, so a regression that staged Wakhan's solution_2 or the subclonal BEDs would still pass. Both stubs now list their staged inputs in `<prefix>/staged.txt` (declared as a stub-only optional output, published like the other files) and the tests assert on it: the top-ranked solution's integer-CN VCF and HP BEDs are picked, nothing from solution_2 or the subclonal set is staged, and SAVANA samples carry their allele counts only when they have them. ASCAT runs for tumour-only samples on dev (Verdict uses it), so `reconplot/severus_ascat` forms for them too: `docs/output.md` said the opposite; fixed, and the ReConPlot stub test gains a tumour-only sample with a tumour-only ASCAT file set (no normal BAF). Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…e --reconplot_regions at start-up A crash in ReConPlot at the end of a whole-genome run failed the whole run through the inherited `errorStrategy 'finish'`. Two ways to trigger it were known: `sanitize_regions()` stopped when every requested region lacked copy-number data, and `run_reconplot.R` exited 1 when it wrote no file. Both are now warnings with exit 0, so an optional focus panel can be absent without failing the task; the required per-chromosome and genome-wide outputs still fail the task when a sample has nothing plottable, which is a real problem and should stop the run. No blanket `errorStrategy 'ignore'`. `--reconplot_regions` is now checked at start-up in `validateSvAnnotationParams()` with the wrapper's grammar (`chr` or `chr:start-end`, start < end), with function tests. Also: the `--baf-track` help no longer says SAVANA only (ASCAT supports it and the pipeline passes it for ASCAT). Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…validator The same preset/annotation logic lived in `workflows/lrsomatic.nf` and in `validateSvAnnotationParams()`, with a comment asking that the two be kept in sync. `padfootGenome()` and `padfootAnnotationOk()` in `utils_nfcore_lrsomatic_pipeline` are now the single source, with function tests for the three presets and the gff/rm requirement. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…the option tables The REVEL licence notice was still on one line with its `[!IMPORTANT]` marker (the first of the two collapsed blocks was fixed in e793b61), so GitHub did not render it as an alert. Tables realigned with the prettier build pre-commit installs (3.9.6). Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
nf-core lint's template_strings check flags `{{index .RepoDigests 0}}` in the
`docker inspect` example as an unrendered template; `docker images --digests`
shows the same digest without braces.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…_text to every new parameter, fix two doc leftovers - The PADFOOT and RECONPLOT module tests now carry the `small` tag that `.github/workflows/nf-test.yml` selects on, so PR CI runs them. - Every `padfoot_*`, `reconplot_*`, `skip_padfoot` and `skip_reconplot` parameter has a `help_text` describing the behaviour that was only in docs/usage.md (gff+rm needed together for non-hg38/mm10 presets, region syntax check and skipping, BAF track applicability, hg38 fallback, conda not supported). - docs/usage.md: removed the sentence that still described the wrapper and package as staged from GitHub and installed under conda. - docs/output.md: the tumour-only tree lists `reconplot/severus_ascat`, which forms for tumour-only samples too. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…T with prebuilt SIF twins Both modules referenced a single `ghcr.io/...@sha256:` digest, so under Singularity/Apptainer the Docker image was converted at first pull, unlike every other custom image in the pipeline (REVIEW.md, "Containers"; automated review findings 3-4). They now use the same ternary as LRSOMATICREPORT and SIGPROFILER, with both branches pinned to one tag: - `oras://ghcr.io/tim-yu/padfoot-repeatmasker-sif:4.2.4-dfam4-padfoot-e7eaed7` / `ghcr.io/tim-yu/padfoot-repeatmasker:4.2.4-dfam4-padfoot-e7eaed7` - `oras://ghcr.io/tim-yu/reconplot-sif:0.2-r4.4` / `ghcr.io/tim-yu/reconplot:0.2-r4.4` The SIFs were built from the published digests (bf134e2f, 1145fc5a) and pushed with ORAS. The container READMEs describe the build + push of both images, and the docs, CHANGELOG and the Dockerfile comment now say "bump the tags" instead of "re-pin the digest". Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
The test profiles produce no copy-number caller output, so no caller pair forms and the two new modules ran only as stubs in CI. tests/fixtures/padfoot_reconplot/ adds invented Severus, Wakhan, ASCAT and SAVANA outputs in each caller's exact file layout on a 2 Mb slice of GRCh38 chr19 (a deletion over STK11 exons with a matching one-copy loss, a tandem duplication with a matching gain, a templated and an Alu insertion, two breakend pairs; regenerated by make_fixtures.py). Five `small` tests run the real script blocks on them: Padfoot on Severus + Wakhan with RepeatMasker on and on SAVANA + SAVANA, ReConPlot on ASCAT + Severus, Wakhan + Severus (the solution_1 re-layout) and SAVANA single-source with the BAF track. They assert on gene hits, impact classes, strand notation and figure names, and snapshot the stable tables and versions. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…, consistent filters Found by an in-depth review of the vendored wrapper on the real P215003155 output and synthetic fixtures: - `--write-tables` wrote coordinates and lengths in scientific notation (`1.2e+08`, `5e+05`); fwrite now uses scipen = 50. - An SV with an undetermined orientation (Severus record without STRANDS and a type other than INS/DEL/DUP, SAVANA notation outside the four symbols) aborted the run in validate_sv instead of being dropped with the others. - Mate records are collapsed on the caller's mate ID when it gives one, with the positional key (now including the orientation) as the fallback; insertions are never collapsed. Mates 1 bp apart no longer draw twice, a ++ and a -- junction on the same breakpoints no longer merge. - `--min-svlen` now applies to SAVANA as well, so the three RECONPLOT tasks of a sample filter alike. - `--genes` symbols are resolved against ReConPlot's gene table first: a symbol with several rows made the package error and lose the whole focus panel; unknown and duplicated symbols are now skipped with a warning. - A failing BAF-track reader (e.g. a het-SNP BED with fewer than 12 columns) skips the track instead of failing the task; `--genome` is validated up front; thousands separators are accepted in `--regions`; regions with end <= start are dropped, duplicates collapsed; the Wakhan BED header is found with or without its comment block; `--source X --cn-input DIR` without `--input` gets a clear error. Cosmetic: CN tables sort chr1, chr2, ... and an empty SV table keeps the parser's column order. VERSION records the local changes on top of the vendored commit. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…idation, skip under conda - `--specie mouse` is ambiguous for RepeatMasker in the shipped Dfam 4.0, so every mm10 run with RepeatMasker on failed; pass "Mus musculus". - `--format` and `--genes` were interpolated unquoted into the ReConPlot command; a value with a space killed the task after the required figures had been written. - validateSvAnnotationParams() accepts thousands separators in --reconplot_regions like the wrapper, no longer throws a stack trace on an unparsable number, and rejects --reconplot_genes with whitespace and --reconplot_format outside pdf/png (also a schema pattern), which would otherwise fail every task with "Missing output file(s)". - Both steps ship only inside their containers: under -profile conda/mamba they are now skipped with a start-up warning instead of failing hours in. - Annotation and figures are downstream of every caller, so a sample they cannot process must not stop a cohort: errorStrategy 'ignore' for PADFOOT_* and RECONPLOT_*. - Tests: the chm13 inference is asserted on its own; the ReConPlot stub tests stage the real wrapper directory. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…t genome-wide clipping, label copy number against the tumour ploidy Images (requested in review: large Apptainer images time out on ghcr): - docker.io/timmy9527/padfoot-repeatmasker:4.2.4-dfam4-padfoot-25fd6d4 and docker.io/timmy9527/reconplot:0.2-r4.4-clipfix, each with an oras:// SIF twin, both branches of the ternary on the same tag. - Padfoot 25fd6d4 bundles the cancer-gene table it used to download on every run (the "nothing is downloaded at run time" claim is now true), pads unlisted Wakhan segments instead of letting genes inherit a neighbour's copy number, keeps the RepeatMasker hits of the last insertion, and fixes the bundled annotation's mislabelled last gene per chromosome. - The ReConPlot Dockerfile pins the package tarball by checksum and patches its clipping step, which compared against the whole chr_selection vector and truncated chr1/chr2 in every genome-wide figure; the build fails if the two lines are not found. Dfam is fetched from the versioned release directory; both Dockerfiles declare the frontend `ADD --checksum` needs. Ploidy: PADFOOT takes the CN caller's fitted purity/ploidy table (Wakhan solutions_ranks.tsv, SAVANA *_fitted_purity_ploidy.tsv) and Padfoot labels each haplotype's integer copy number against ploidy/2, rounding SAVANA's fractional values first. On P215003155 the SAVANA pair's by_gene.tsv went from 17,209 to 30 genes with both haplotypes "deleted" and the Wakhan pair from 11,941 to 450; the SV tables are unchanged. The subworkflow joins the fit tables with remainder: true, so a missing table never drops a pair; the harness and all tests pass them; the real Padfoot test asserts the RepeatMasker class and the ploidy-driven labels. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
docs/usage.md: Docker Hub references, SIF sizes in the offline paragraph, how gene copy number is labelled against the fitted ploidy. docs/output.md: the SV table's real columns, by_gene semantics. README: the tumour-only tree gains reconplot/severus_ascat (ASCAT runs tumour-only). meta.yml of both modules describes the stub-only `staged` output and the new ploidy input. Container READMEs describe building and publishing both images on Docker Hub. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…abels and known-fusion detection Two more Tim-Yu/Padfoot commits on top of 25fd6d4, both fixing behaviour inherited from upstream: - f8c9e5d: the breakpoint-to-gene lookup compared two bisect positions on lists that are not both sorted, so on P215003155 it left 66 of 660 Severus + Wakhan and 44 of 560 SAVANA breakpoints without the gene they lie in (FGFR3, LETM1, SPPL2B, ...). The new containment search agrees with an independent brute-force lookup on every breakpoint. It also finishes relabelling the bundled annotations' misplaced last genes (FRG2B, MZF1, PRMT2, RABL2B). - 3846215: flank breakpoints were labelled as introns and intron numbers kept only their last digit (132 of 256 labels wrong), which could turn a multi-exon deletion into `intronic`; the in-frame test used `//` instead of `%`; the known-fusion lookup never fired. On P215003155 both callers now report COL1A1::PDGFB as an oncogenic fusion. Image docker.io/timmy9527/padfoot-repeatmasker:4.2.4-dfam4-padfoot-3846215 (+ -sif). The real PADFOOT tests now pin the STK11 deletion as `between_exons` (intron 3 -> exon 10) and the minus-strand SBNO2 flank as `downstream`. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…thout a solution
Found in the 23-pair cohort run:
- ReConPlot adds one plot layer per SV, so on a chromosome with a few thousand SVs R runs out of
its node stack ("node stack overflow"; the stack size is fixed at build time and disabling the
JIT does not help). The wrapper already logged such a figure and went on, but genome_wide was a
required output, so the task failed and its other figures were lost (P215002781: 44 drawn
per-chromosome figures discarded). All figure outputs are now optional and the task fails only
when no figure at all was drawn.
- ASCAT writes an empty segments.txt when it finds no solution (P215002180); the parser crashed in
fread. RECONPLOT_FIGURES now skips the ASCAT pair for such a sample, and the wrapper stops with
a clear message if it is run on one directly.
The subworkflow stub test gains a sample whose ASCAT found no solution; docs/output.md describes
both behaviours.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
dev moved WAKHAN to 0.5.0 (IntGenomicsLab#214), whose module no longer has `vcf_files` / `bed_files`: each solution is one `solution_<ploidy>_<purity>_<conf>/` directory with a merged `integer_profile.{bed,vcf}`, and `solution_rank_N` links rank them. With Wakhan on (the default) the pipeline aborted at launch ("No such property: vcf_files" / "bed_files"); CI could not see it because the test profiles skip Wakhan. - Both subworkflows take `WAKHAN.out.solution_dirs` and use `solution_rank_1`: Padfoot gets its `integer_profile.vcf` (same CN1/CN2/COV1 format Padfoot reads), ReConPlot its `integer_profile.bed` plus `solutions_ranks.tsv`. - The wrapper's Wakhan parser reads the merged profile (hp1_/hp2_copynumber_state; unphased copynumber_state too) and keeps the 0.4 layout as a fallback; the module's bed_output relayout is gone. - PADFOOT_ANNOTATION: a fit table without a matching SV/CN pair arrives as a right-only row of the remainder join and crashed the 4-argument closure; both branches now filter on row[1]. - Fixtures regenerated in the 0.5.0 layout (`wakhan/solution_rank_1/integer_profile.{bed,vcf}`, `wakhan/solutions_ranks.tsv`), headers as Wakhan 0.5.0 writes them; the stub tests use ranked solution directories and cover the right-only rows (a sample with ranks but no rank-1 profile, a SAVANA fit table without copy number). - tests/sv_annotation_compose.nf.test (`small`): `-preview` of the test profile with Wakhan, ASCAT, Padfoot and ReConPlot on, so a renamed or removed caller output fails CI at launch. It fails on the previous wiring with exactly the launch error. Checked on a real Wakhan 0.5.0 run of P215003155 (the dev module on the September inputs): both subworkflows run through the real solution_rank_1 link; the ReConPlot CN table and Padfoot's gene table differ from the 0.4-based ones only by Wakhan's own calling changes (a chr8 haplotype swap, 7 segment states on chr12/chr17). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…NA figures without SVs, check --padfoot_genome
From the independent review of the branch:
- errorStrategy 'ignore' on PADFOOT_* / RECONPLOT_* had replaced base.config's retry on resource
kills (130-145, 104, 175-177); those are now retried first, then ignored.
- Padfoot passes the RepeatMasker species unquoted, so "Mus musculus" split into two arguments
("Ambiguous search term 'Mus'"); mm10 now uses mus_musculus, which the image resolves to taxid
10090 (the Dockerfile smoke test uses the same term).
- SAVANA writes an empty classified.somatic.bedpe for a sample without somatic SVs; the wrapper
stopped ("fewer than 7 columns") and the sample lost its SAVANA figures. An empty BEDPE is now
an empty SV set.
- --padfoot_genome on another assembly than --genome (e.g. hg38 on CHM13) silently annotated T2T
coordinates with hg38 genes; it is now an error at start-up, and the skip warning no longer
suggests it. Two function tests.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…repeats, robust Wakhan input Six Tim-Yu/Padfoot commits on top of 3846215, from the independent review and its follow-ups: - --gff / --rm (the route for CHM13 and other genomes without bundled annotations) crashed three ways: relative paths after Padfoot's chdir, the RepeatMasker .out / BED parsing, and a gzip read/write mismatch. They now take a GENCODE-style GFF3 (plain or gzipped) and a RepeatMasker .out or a chr/start/end/class BED; on the fixture they reproduce the bundled hg38 annotation. - External commands are quoted, so a species such as "Mus musculus" no longer splits. - temp_bps.bed was not closed before bedtools read it, so breakpoint repeat classes were lost after the last flushed 8 KiB block: on P215003155, 28 Severus and 44 SAVANA SVs gain their Repeat_Anno, checked against an independent scan of the bundled repeat file; nothing else in the tables changes. - A header-only Wakhan VCF (copy-neutral tumour) and a very low per-copy coverage no longer crash; contig lengths for the copy-number padding fall back to the reference .fai; the mm10 hint names mus_musculus; insertion alignments are written in a fixed order (they followed the hash seed). Image docker.io/timmy9527/padfoot-repeatmasker:4.2.4-dfam4-padfoot-1748e84 (+ -sif). A new real PADFOOT test runs the custom-annotation route with the chm13 preset on fixtures in tests/fixtures/padfoot_reconplot/custom_annotation/; the docs and schema describe the accepted formats and that --padfoot_genome must match --genome. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…de /home, non-fatal focus panel, cache and gate fixes - PADFOOT stub: `printf '%s\n'` in the GString put a real newline into .command.sh, so the indented heredoc never closed and versions.yml was malformed; any -stub run with Padfoot failed in softwareVersionsToYAML. The stub snapshots recorded the broken file. - Padfoot image 4.2.4-dfam4-padfoot-1748e84-r2 (same Padfoot commit): Dfam moved from /home/mambauser/dfam to /opt/conda/envs/padfoot/share/dfam. With /home bound into the container (site singularity.conf or runOptions) RepeatMasker failed and every Padfoot result was silently ignored; checked with -B <empty>:/home on both images. The image records PADFOOT_COMMIT, which versions.yml now reports (Padfoot's own version string never changes). - ReConPlot: the optional focus panel no longer fails the task (a failure is logged and the per-chromosome and genome-wide figures are kept, as the docs say); an empty region list is no longer a crash in the wrapper and is rejected at start-up; --reconplot_genes is checked against a symbol pattern (a quote broke the command line) and both it and --reconplot_baf_track warn when set without --reconplot_regions. - -resume: the wrapper directory is cached on its top level only, so a change under R/ reused stale figures; a digest of the wrapper files now goes into its meta map. - Padfoot/ReConPlot are skipped (with a start-up warning) when no container engine is in use, not only under the conda/mamba profiles. - Tests: two ReConPlot tests run the pipeline's own arguments with a focus panel (thousands separators, an unknown gene, the BAF track) and a failing focus panel; two validator tests. Docs: the Severus SV table columns. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…graph The -preview tests only asserted that the run composed, which is also true when a gate silently drops Padfoot or ReConPlot. They now write the workflow graph (-with-dag dag.mmd) and assert on its process nodes: with Padfoot on, both PADFOOT_* and all three RECONPLOT_* steps and their callers must be present; with --skip_padfoot, no PADFOOT_* step and all three RECONPLOT_* steps. Checked against deliberately broken copies of the branch: the tests now fail when Padfoot's genome gate or the container-engine gate is wrongly false and when --skip_padfoot is ignored (the old tests passed the first of these), and still fail at launch on the pre-Wakhan-0.5.0 wiring. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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…test Re-align the fixture README table as prettier writes it, keep the Wakhan fixture BED's empty last column (a trailing tab, as Wakhan writes it) out of the whitespace trimmer, and exempt the -preview pipeline test from the versions.yml snapshot rule: a preview run publishes nothing, so it asserts on the workflow graph instead. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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thanks for the approval. The containers are now on Docker Hub. Before you merge, though, the head has changed a lot since you approved.
Thank you so much |
SAVANA writes <id>.classified.somatic.bedpe only from its model classifier
(ONT). With --pb, `savana classify` and `savana to` run classify_pacbio,
which writes the classified somatic VCF alone. RECONPLOT_FIGURES joined on
the BEDPE, so every PacBio sample, paired or tumour-only, silently lost its
reconplot/savana figures (seen on the C8 PacBio pair).
- RECONPLOT_FIGURES takes the classified somatic VCF, which SAVANA writes on
every platform and Padfoot already reads; the now-unused somatic_bedpe
emits leave PAIRED_SAVANA / TUMORONLY_SAVANA.
- Wrapper: --sv-format defaults to auto (the BEDPE when staged, else the
VCF). On a real ONT sample (BL1, 2,084 junctions) both give the same
junctions and CN table; only an insertion's second position differs by
the 1 bp SAVANA's BEDPE adds. VERSION bumped.
- New RECONPLOT module test for the VCF-only case.
- The PADFOOT_ANNOTATION / RECONPLOT_FIGURES stub tests call their local
closures with .call(): Nextflow >= 26.04 strict syntax rejects mk(...)
("`mk` is not defined"), which failed the latest-everything shards
(hidden by continue-on-error).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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I pushed 5453919 to this branch. It fixes something a real-data check turned up: PacBio samples never got Cause. SAVANA writes Change.
Also in this commit. The Checked on Mindwell (Apptainer).
🤖 Generated with Claude Code |
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@claude review |
| // Padfoot and ReConPlot ship only inside their containers (validateSvAnnotationParams() warns under conda/mamba) | ||
| def sv_annot_container_ok = workflow.containerEngine != null | ||
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| if (!params.skip_padfoot && padfoot_annot_ok && sv_annot_container_ok) { |
There was a problem hiding this comment.
Test coverage (REVIEW.md → Tests): no small test runs a task through this wiring. conf/test.config and conf/test_full.config skip Padfoot/ReConPlot, tests/sv_annotation_compose.nf.test uses -preview only (it builds the DAG and runs no tasks), and the subworkflow tests feed hand-made channels under -stub.
So these paths are never exercised with real upstream output:
- the real
WAKHAN.out.solution_dirs, wheresolution_rank_1is a symlink tosolution_<ploidy>_<purity>_<conf>/. The subworkflows callbest.resolve('integer_profile.vcf'|'.bed').exists()on it on the head node, and if that resolves to false the pair is silently dropped rather than failing; - the real
ASCAT.out.bafs/segmentsfile names that the wrapper picks by name; errorStrategy 'ignore'inconf/modules.config. A Padfoot/ReConPlot failure in a real run shows up as missing output, not as a red CI.
Please run the Slurm test array (whole-genome paired + tumour-only, GRCh38 and CHM13) with --skip_padfoot false --skip_reconplot false. Then confirm that <sample>/padfoot/{severus_wakhan,savana} and <sample>/reconplot/{severus_ascat,severus_wakhan,savana} contain real tables and figures, and that no task was ignored.
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Automated review: 1 finding.
For a human reviewer to check by running the pipeline:
Non-blocking notes:
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Summary
Adds two downstream steps for the SV and copy-number callers already in the pipeline, as discussed in #192:
<sample>/padfoot/{severus_wakhan,savana}/.<sample>/reconplot/{severus_ascat,severus_wakhan,savana}/.Both run by default and are switched off with
--skip_padfoot/--skip_reconplot.PAIRED_SAVANAandTUMORONLY_SAVANAgain three emits (somatic BEDPE, fitted purity/ploidy, het-SNP allele counts) that the two steps consume; no other change to the SAVANA stack from #189.Design notes
KolmogorovLab/Padfootthat adds SAVANA input (I will propose it upstream;--padfoot_dirtakes a local checkout). The ReConPlot wrapper (run_reconplot.R+ parsers for ASCAT, Wakhan, Severus and SAVANA) ships inassets/reconplot/; the ReConPlot R package is fetched from a pinned upstream commit because-profile condainstalls it at run time.ghcr.io/tim-yu/padfoot-repeatmasker(Padfoot deps + RepeatMasker 4.2.4 + Dfam 4.0) andghcr.io/tim-yu/reconplot(R + ReConPlot), both digest-pinned in the modulecontainerdirectives sonf-core pipelines downloadstages them. Recipes undercontainers/. Under conda, RepeatMasker uses the curated Dfam subset bundled with bioconda.<sv_caller>_<cn_caller>for both tools. SAVANA's own output stays where Add savana module #189 put it (variants/savana).Testing
nextflow lint: no new warnings (15 ondev, 15 here).pre-commit/prettier clean.nf-core pipelines lint: 0 failed.tests/default.nf.testpasses under Singularity with the snapshot unchanged (Padfoot and ReConPlot need whole-genome caller output, so-profile testandtest_fullskip them).-stubnf-tests for both subworkflows (tagsmall, so they run on every PR) check that each caller pair is formed for the right samples and that samples lacking one side are dropped. Module-level nf-tests forPADFOOTandRECONPLOT(stub).dev@ 0cf00bf, 2026-09-23):nextflow lintidentical todev;nf-test --tag small --profile +singularity39/39; the two modules driven through their real subworkflows on whole-genome Severus/Wakhan/ASCAT/SAVANA output of a 40x ONT pair reproduce the earlier run byte-for-byte (tables, gene lists, figure counts); chr22 paired + tumour-only end-to-end 75/75 tasks. A whole-genome paired run from raw uBAMs with every tool on (Padfoot, ReConPlot, SAVANA, Wakhan, ASCAT, VEP, modkit, report) is in progress. Hopufully finishing soon and will update.minimap2-> Clair3/ClairS/ClairS-TO -> LongPhase -> Severus + SAVANA -> Padfoot -> ReConPlot), twice on this branch. On the merged tree SAVANA finds no acceptable purity/ploidy fit for either chr22 sample (it did for the tumour-only sample on the pre-merge ClairS-TO 0.4.2 calls), so these runs prove the skip path: the joins drop the samples and the pipeline completes. The positive path is proven on whole-genome caller output of a 40x ONT pair (Severus, Wakhan, ASCAT, SAVANA): Padfoot with RepeatMasker on both pairs, ReConPlot on all three pairs including the focus panel with gene labels and BAF track, using the vendored wrapper.Known limitations / follow-ups
IntGenomicsLab/test-datasetsif you want them.-stub-runcurrently fails before reaching these steps (theCRAMINOstubs lack*.arrow, the nf-corelongphase/phasestub runstabixon a file it never creates, and theWAKHANandSEVERUSstubs create fewer or differently named files than they declare). Out of scope here; happy to send a separate PR.PADFOOT_ANNOTATIONandRECONPLOT_FIGURESfetch their sources (90 MB + 30 MB) at run start even when no caller pair forms for any sample; harmless, could be guarded on non-empty input.--chromosomesfrom the contigs list, and a few unexposed CNA knobs (which was implemented in my previous attempts of local savana module).PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).For sure generated with Claude Code and then audited by Boyu.