Qc optimization #1601
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Qc optimization #1601
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- Set skip_dupradar=true (mostly pointless for bulk RNA-seq) - Set skip_qualimap=true (identified as slowest QC step) - Set skip_rseqc=true (7 resource-intensive modules by default) - Set skip_stringtie=true (additional assembly overhead) - Set skip_bigwig=true (coverage track generation overhead) Follows nf-core/proposals#71 to make QC steps opt-in rather than mandatory. Users can re-enable comprehensive QC via parameters when needed. Significantly reduces pipeline runtime and compute costs for standard bulk RNA-seq workflows. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com> Co-Authored-By: adamrtalbot <adamrtalbot@users.noreply.github.com>
Add comprehensive documentation for the performance-optimized QC defaults: - Add "Quality Control Configuration" section to usage.md explaining the v4.0 changes - Document which QC steps are now disabled by default and why - Provide clear commands to restore comprehensive QC when needed - Add guidance on when to enable extended QC analysis - Update all affected QC sections in output.md with proper admonition notes - Use consistent :::note syntax following nf-core documentation standards Updates changelog with breaking changes and performance improvements. Helps users understand the new defaults and migrate their workflows appropriately. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
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pinin4fjords
requested changes
Sep 1, 2025
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| Starting in version 4.0, several QC steps are disabled by default to improve pipeline performance and reduce compute costs for typical bulk RNA-seq analysis: | ||
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| - **`--skip_dupradar true`** - Disable dupRadar analysis (limited utility for bulk RNA-seq experiments) |
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Could you qualify the reasoning behind the 'limited utility' assertion please?
| Starting in version 4.0, several QC steps are disabled by default to improve pipeline performance and reduce compute costs for typical bulk RNA-seq analysis: | ||
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| - **`--skip_dupradar true`** - Disable dupRadar analysis (limited utility for bulk RNA-seq experiments) | ||
| - **`--skip_qualimap true`** - Disable Qualimap alignment QC (resource-intensive step) |
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Since we're flipping the sense of the flags (and we'd have to make a major version anyway), maybe these should be renamed instead? --run_qualimap etc?
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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).