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Export per-mutation signature probabilities from SigProfilerAssignment - #221
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Addresses #127 (comment 4809238681): export_probabilities_per_mutation only works with VCF input, so the COSMIC fit now reads the PASS VCF; the matrices only gate which contexts are fitted. cosmic_fit ignores --volume, so the genome volume is set through SIGPROFILER{MATRIXGENERATOR,ASSIGNMENT}_VOLUME. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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| input_${ctx}/ \\ | ||
| ${prefix}/${ctx} \\ | ||
| --input_type matrix \\ | ||
| --input_type vcf \\ |
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No small test runs this script block. CI only runs the stub test, which just touches the output files. The pipeline tests set skip_signatures = true in both conf/test.config and conf/test_full.config. So none of the new behaviour is exercised:
--input_type vcfwith--context_type 96|DINUC|ID- SigProfilerAssignment's internal matrix generation, which finds the genome only through
SIGPROFILERMATRIXGENERATOR_VOLUMEand needstsb/${genome}. Only that one genome is linked intovolume/. Check that the ID fit, whose signatures are GRCh37-based, doesn't try to load or installtsb/GRCh37on a GRCh38 or CHM13-T2T run. --export_probabilities_per_mutation Truewith the DBS78 and ID83 fits, not just SBS96.
Please run the Slurm test array (or a real signatures run on GRCh38 and on CHM13) and confirm that Decomposed_Mutation_Probabilities/ is filled in for every fitted context.
| --cosmic_version ${cosmic_version} \\ | ||
| --collapse_to_SBS96 ${collapse} \\ | ||
| --volume spa_volume \\ | ||
| --export_probabilities_per_mutation True \\ |
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Missing CHANGELOG.md entry. This PR adds a new published output (Decomposed_Mutation_Probabilities/) and switches the COSMIC fit from matrix input to VCF input, which can change the fitted activities. CHANGELOG.md has no entry for #221 under v1.2.0dev. REVIEW.md requires one.
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Automated review: 2 findings (see inline comments).
To check by running: the Slurm test array or a real signatures run on GRCh38 and on CHM13-T2T. Confirm that |
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…ities from seqinfo VCF-mode cosmic_fit re-ran MatrixGenerator without the user's matrix args, so --bed_file/--exome filtered the published matrices but not the fit, and each context re-checksummed the genome. The fit reads the matrices again and the per-mutation table comes from probabilities_per_mutation() on the MatrixGenerator seqinfo, so the genome volume input is dropped. - Reject --bed_file, --exome and --seqInfo False in --sigprofiler_matrix_args - Add non-stub small nf-tests on synthetic matrices for GRCh38 and CHM13-T2T - CHANGELOG entries and output/usage docs for the new output Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Addresses #127 (comment 4809238681): export_probabilities_per_mutation only works with VCF input, so the COSMIC fit now reads the PASS VCF; the matrices only gate which contexts are fitted. cosmic_fit ignores --volume, so the genome volume is set through SIGPROFILER{MATRIXGENERATOR,ASSIGNMENT}_VOLUME.
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).