upgrade 0.7.0 #13
upgrade 0.7.0 #13
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Pull Request Overview
This PR upgrades the SASH pipeline to version 0.7.0 with major updates including PCGR 2.2.1 integration, mutational signature analysis via SIGRAP, improved hypermutation handling, and VCF2MAF support for OncoAnalyser V2.2.0 compatibility.
Key Changes:
- Integrated SIGRAP mutational signature analysis modules (hrdetect, mutpat, chord)
- Updated PCGR from version 20220203 to 20250314 with separate VEP directory configuration
- Updated BOLT container versions to support new PCGR and reporting features
Reviewed Changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/sash.nf | Main workflow integration of SIGRAP processes and updated cancer report inputs |
| subworkflows/local/sigrap_analysis.nf | New subworkflow orchestrating SIGRAP chord, hrdetect, and mutpat analyses |
| subworkflows/local/prepare_input.nf | Added CHORD prediction TSV input channel preparation |
| modules/local/sigrap/mutpat/main.nf | New SIGRAP mutpat process for mutational pattern analysis |
| modules/local/sigrap/hrdetect/main.nf | New SIGRAP hrdetect process for HRD detection |
| modules/local/sigrap/chord/main.nf | New SIGRAP chord process wrapper |
| modules/local/bolt/sv_somatic/prioritise/main.nf | Container version update to 0.3.0-dev-6 |
| modules/local/bolt/smlv_somatic/report/main.nf | Added VEP directory parameter and updated PCGR output filename |
| modules/local/bolt/smlv_somatic/annotate/main.nf | Added VEP directory parameter |
| modules/local/bolt/smlv_germline/report/main.nf | Added VEP directory parameter |
| modules/local/bolt/other/cancer_report/main.nf | Added SIGRAP inputs and updated container version |
| conf/refdata.config | Updated PCGR version and added VEP directory configuration |
| conf/modules.config | Updated PCGR filename pattern and added SIGRAP publish directories |
| .github/workflows/docker-build.yml | New workflow for automated Docker container builds |
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| stub: | ||
| """ | ||
| mkdir -p output/ |
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The stub creates an unused 'output/' directory. This should be removed as it doesn't match the actual output path pattern used in the script block.
| mkdir -p output/ |
| if (filename.equals('versions.yml')) { | ||
| return null | ||
| } else { | ||
| println "SIGRAP_MUTPAT - meta.key: '${meta.key}', filename: '${filename}'" |
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Debug println statement should be removed before merging to production. This will generate console output on every file publication.
| println "SIGRAP_MUTPAT - meta.key: '${meta.key}', filename: '${filename}'" |
| ch_sv_somatic_sv_vcf_out, | ||
| ch_sv_somatic_cnv_tsv_out, | ||
| ) | ||
| .map { meta, smlv_vcf, sv_vcf, cnv_tsv -> |
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Trailing whitespace detected at the end of this line. Should be removed for consistency.
| .map { meta, smlv_vcf, sv_vcf, cnv_tsv -> | |
| .map { meta, smlv_vcf, sv_vcf, cnv_tsv -> |
| id: meta.id, | ||
| tumor_id: meta.tumor_id, | ||
| ] | ||
| return [meta_sigrap, smlv_vcf, sv_vcf, cnv_tsv] |
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Trailing whitespace detected at the end of this line. Should be removed for consistency.
| return [meta_sigrap, smlv_vcf, sv_vcf, cnv_tsv] | |
| return [meta_sigrap, smlv_vcf, sv_vcf, cnv_tsv] |
| id: meta.id, | ||
| tumor_id: meta.tumor_id, | ||
| ] | ||
| return [meta_sigrap, vcf] |
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Trailing whitespace detected at the end of this line. Should be removed for consistency.
| return [meta_sigrap, vcf] | |
| return [meta_sigrap, vcf] |
| // channel: [ meta, hrdetect_json ] | ||
| ch_hrdetect_out = WorkflowSash.restoreMeta(SIGRAP_HRDETECT.out.hrdetect_json, ch_inputs) | ||
| ch_versions = ch_versions.mix(SIGRAP_HRDETECT.out.versions) | ||
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Line contains only trailing whitespace. Should be removed for consistency.
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duplicate #39 |
Individual PR
ready
Change outside of Sash
Add reference data to prod
Update gpgr
Update sigrap