Important! Template update for nf-core/tools v3.5.1 #1628
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- Keep dev version with blank line in release-announcements.yml - Keep dev version of ro-crate-metadata.json with established pipeline content - Reject template's samplesheet processing in PIPELINE_INITIALISATION - Delete template stub workflows/rnaseq.nf file 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Merged with latest dev CHANGELOG entries 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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pinin4fjords
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Nov 25, 2025
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Just checking with @ewels on why the 'check-heatmap' files are no longer produced in MultiQC 1.32 before we merge this. |
pinin4fjords
dismissed
their stale review
want to check on the multiqc thing
The FastQC status check heatmaps (PNG/SVG) are no longer produced by the updated version of MultiQC from the template update 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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MultiQC v1.32 (from the template update) no longer produces FastQC status check heatmap PNG/PDF/SVG files, possibly related to the Bootstrap 5 upgrade in that release. Reverting to MultiQC v1.31 (git_sha e10b76ca0c66213581bec2833e30d31f239dec0b) until the change in behavior is better understood, and restoring the test snapshots that expect these files to be present. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
The template merge updated this subworkflow but it was incorrectly reverted along with MultiQC. This commit updates only the utils_nfcore_pipeline git_sha to the v3.5.1 version while keeping MultiQC at v1.31.
pinin4fjords
approved these changes
Nov 25, 2025
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Version
3.5.1of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2025/tools-3_5_0For more information about this release of nf-core/tools, please see the
v3.5.1release page.Template Merge Resolution Summary
Resolution Strategy
All merge conflicts were resolved by preserving pipeline-specific features and established content while adopting template infrastructure improvements where appropriate. The template's simplified samplesheet processing was rejected in favor of the existing complex implementation that supports BAM file inputs.
Template Infrastructure Improvements (Adopted)
Pipeline-Specific Features (Retained)
ro-crate-metadata.json: Kept dev version with complete pipeline-specific README content, established dates, and existing UUIDs rather than template's auto-generated placeholders
PIPELINE_INITIALISATION workflow: Rejected template's simplified samplesheet processing logic. The pipeline uses more complex samplesheet handling in the main RNASEQ workflow that supports:
checkSamplesAfterGroupingfunctionworkflows/rnaseq.nf: Removed template stub file - pipeline uses
workflows/rnaseq/main.nfwith full implementationFiles with Conflicts Resolved
.github/workflows/release-announcements.yml- Simple whitespace conflict, kept dev version with blank line for readabilityro-crate-metadata.json- Kept dev version with pipeline-specific contentsubworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf- Rejected template's samplesheet processingworkflows/rnaseq.nf- Deleted template stub file (modify/delete conflict)Additional Notes