Add subworkflow for gridss somatic structural variant calling - #12574
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imsarath wants to merge 8 commits into
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Add subworkflow for gridss somatic structural variant calling#12574imsarath wants to merge 8 commits into
imsarath wants to merge 8 commits into
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SPPearce
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Aug 18, 2026
SPPearce
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Aug 19, 2026
SPPearce
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Can you format the main.nf with each module argument on its own line too please
SPPearce
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Aug 28, 2026
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| { assert snapshot( | ||
| path(workflow.out.gridss_vcf[0][1]).vcf.summary, | ||
| workflow.out.all_somatic_vcf.collect { meta, vcf -> [ meta, file(vcf).name ] }, | ||
| workflow.out.high_confidence_somatic_vcf.collect { meta, vcf -> [ meta, file(vcf).name ] } | ||
| ).match() } |
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Try this (untested):
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| { assert snapshot( | |
| path(workflow.out.gridss_vcf[0][1]).vcf.summary, | |
| workflow.out.all_somatic_vcf.collect { meta, vcf -> [ meta, file(vcf).name ] }, | |
| workflow.out.high_confidence_somatic_vcf.collect { meta, vcf -> [ meta, file(vcf).name ] } | |
| ).match() } | |
| { assert snapshot(sanitizeOutput(workflow.out, variantsMD5Keys: ["gridss_vcf", "all_somatic_vcf", "high_confidence_somatic_vcf"]).match() } |
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A couple of comments.
You should be able to calculate is_targeted based on whether ch_target_bed exists?
Should the input tuple be flatter, rather than [tumour_bam, normal_bam] as a nested tuple.
Should the target bed be part of the input tuple? I could see scenarios where you are only interested in certain variants per sample.
What happens if you have more than one tumour sample per normal sample, can the subworkflow deal with that?
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This PR adds
bam_tumor_normal_somatic_structural_variant_calling_gridss, a subworkflow that calls somatic structural variants from a tumor/normal BAM pair. It chains the full GRIDSS workflow - optional targeted fragment extraction, per-sample preprocess, joint assembly and call, thengridss_somatic_filter. It emits the unfiltered joint VCF plus the all-somatic and high-confidence somatic call sets.PR checklist
Closes #4498
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda