Apply 2.0.1 to dev#161
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Release 2.0
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
Adjust memory configuration for VCF and GVCF stats reports
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Pull request overview
This PR syncs the dev branch with the 2.0.1 patch release metadata and introduces dynamic memory sizing for the DeepVariant vcf_stats_report steps based on input VCF size.
Changes:
- Add per-input-size memory calculation for
VCF_STATS_REPORTandGVCF_STATS_REPORTin the base config. - Bump pipeline version references from
2.0.0to2.0.1across Nextflow manifest, RO-Crate metadata, citation, changelog, nf-test snapshots, and nf-core metadata. - Minor workflow comment clarification about merging by sample/specimen name.
Reviewed changes
Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/variantcalling.nf | Clarifies comment about merge semantics (sample/specimen). |
| conf/base.config | Adds dynamic memory sizing for VCF/GVCF stats report processes. |
| nextflow.config | Bumps manifest version to 2.0.1. |
| ro-crate-metadata.json | Updates published/modified timestamps and versioned URLs to 2.0.1. |
| CITATION.cff | Updates release date/title/version to 2.0.1. |
| CHANGELOG.md | Adds 2.0.1 entry documenting memory adjustment. |
| .nf-core.yml | Updates recorded version to 2.0.1. |
| tests/default.nf.test.snap | Updates expected workflow version string to v2.0.1. |
| tests/align.nf.test.snap | Updates expected workflow version string to v2.0.1. |
Comments suppressed due to low confidence (1)
conf/base.config:83
- Same issue as
VCF_STATS_REPORT: if the input file is 0 bytes (possible in stub runs or edge cases),Math.ceil(vcf.size()/...)returns 0 and the memory directive becomes 0.GB, which can make Nextflow error out. Ensure the computed memory is always >= a sensible minimum by clamping the size factor to at least 1.
withName: GVCF_STATS_REPORT {
// keep cpus,time from process_single, define memory based on input size
memory = { 1.GB * Math.ceil( vcf.size()/15000000 ) * task.attempt }
}
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| memory = { 1.GB * Math.ceil( vcf.size()/30000000 ) * task.attempt } | ||
| } | ||
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| withName: GVCF_STATS_REPORT { | ||
| // keep cpus,time from process_single, define memory based on input size | ||
| memory = { 1.GB * Math.ceil( vcf.size()/15000000 ) * task.attempt } |
muffato
approved these changes
May 15, 2026
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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).