Fix consensus calling to include all variant callers#2096
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FriederikeHanssen merged 24 commits intodevfrom Jan 18, 2026
Merged
Fix consensus calling to include all variant callers#2096FriederikeHanssen merged 24 commits intodevfrom
FriederikeHanssen merged 24 commits intodevfrom
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Fixes #2088 The consensus calling feature was missing several variant callers from the list of tools eligible for normalization and consensus processing. This caused VCFs from bcftools (mpileup) and lofreq to be excluded from consensus calling, even when specified by the user. Additionally, the Sentieon tool names in the list were incorrect (using short names like 'dnascope' instead of actual names 'sentieon_dnascope'). Changes: - Add 'bcftools' and 'lofreq' to small_variantcallers list - Fix Sentieon tool names to match actual variantcaller metadata: - 'dnascope' → 'sentieon_dnascope' - 'haplotyper' → 'sentieon_haplotyper' - 'tnscope' → 'sentieon_tnscope' - Remove non-existent 'haplotyper' entry (was never used) Impact: Users can now properly run consensus calling with all supported variant callers including lofreq and mpileup (bcftools). Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
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Fixes #2088 The consensus calling feature was missing several variant callers from the list of tools eligible for normalization and consensus processing. This caused VCFs from bcftools (mpileup) and lofreq to be excluded from consensus calling, even when specified by the user. Additionally, the Sentieon tool names in the list were incorrect (using short names like 'dnascope' instead of actual names 'sentieon_dnascope'). Changes: - Add 'bcftools' and 'lofreq' to small_variantcallers list - Fix Sentieon tool names to match actual variantcaller metadata: - 'dnascope' → 'sentieon_dnascope' - 'haplotyper' → 'sentieon_haplotyper' - 'tnscope' → 'sentieon_tnscope' - Remove non-existent 'haplotyper' entry (was never used) - Add comprehensive inline documentation explaining the list - Add runtime validation to warn about unknown variant callers - Update consensus test to include lofreq and mpileup - Update CHANGELOG Impact: Users can now properly run consensus calling with all supported variant callers including lofreq and mpileup (bcftools). If a new SNV caller is added in the future and not added to the list, a warning will be logged. Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
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maxulysse
approved these changes
Jan 13, 2026
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failing tests aside. I tested this on some real tumor-only data now and it seems to work |
Add ignoreFiles patterns to exclude non-deterministic consensus outputs: - 0000.vcf.gz and 0000.vcf.gz.tbi (consensus VCF files) - sites.txt (bcftools isec sites file) These files have unstable MD5 checksums and VcfFile metadata that change between runs, so they must be excluded from snapshot assertions while still appearing in the file list. Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
Add patterns to exclude unstable consensus calling outputs: - variant_calling/consensus/*/*/0000.vcf.gz* - variant_calling/consensus/*/*/sites.txt These bcftools isec outputs are non-deterministic and produce different checksums between runs. Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
Fix nested braces in glob pattern that caused PatternSyntaxException.
Changed from {0000.vcf{,.gz},sites.txt} to {0000.vcf,0000.vcf.gz,sites.txt}
to avoid nesting groups.
Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
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should close #2088
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).