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Co-authored-by: Claude Opus 4.5 <[email protected]> Fixes #2079 fix applied in #1858 for other optional reference files
This reverts commit 53958c6.
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When starting from `--step variant_calling` with BAM files that include a `lane` column in the samplesheet, the meta.id was set to `sample-lane` (e.g. "PM10_P0-1"). However, the Mutect2 tumor-only subworkflow resets the ID to `meta.sample` (e.g. "PM10_P0") at the pileup/contamination step. This mismatch caused the `.join()` to produce an empty channel, so FilterMutectCalls silently never ran. The fix uses lane-based IDs only for the mapping step (where lanes are processed separately). For all other steps, the sample-based ID is used, ensuring consistent ID matching in downstream channel joins. Co-Authored-By: Claude Opus 4.6 <[email protected]>
Co-Authored-By: Claude Opus 4.6 <[email protected]>
Co-Authored-By: Claude Opus 4.6 <[email protected]>
Update snpsift/annmem and install snpsift/annmemcreate from nf-core modules. Adapt subworkflows and config for the new separate modules. Co-Authored-By: Claude Opus 4.6 <[email protected]>
The withName selector included a trailing :ENSEMBLVEP_VEP after the VCF_ANNOTATE_MERGE alias, which no longer matches in Nextflow 25.10.3. Drop the suffix so the merge-specific prefix config is applied correctly. Co-Authored-By: Claude Opus 4.6 <[email protected]>
FEAT: Add topics for versions
feat: snpsift//annotatemem
Fix FilterMutectCalls not running when starting from BAM with lane field
Improve filename for snpSift
maxulysse
approved these changes
Feb 10, 2026
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Waiting for #2101
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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).