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Pull request overview
This PR aims to incorporate NanoPlot outputs into the pipeline’s MultiQC report, while also improving NanoPlot output file naming to avoid collisions and improve sample identification.
Changes:
- Add NanoPlot
*.txtoutputs (pre- and post-alignment) to the set of files collected for MultiQC. - Prefix NanoPlot output filenames using
task.ext.prefixto make outputs sample-specific. - Adjust module config to set prefixes for Cramino/NanoPlot and avoid publishing
.arrowintermediates.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
workflows/lrsomatic.nf |
Adds NanoPlot text outputs into the MultiQC input collection. |
modules/nf-core/nanoplot/main.nf |
Renames NanoPlot outputs with a configurable prefix to improve uniqueness/sample labeling. |
conf/modules.config |
Configures prefixes and publishing behavior for Cramino/NanoPlot outputs (including suppressing .arrow publish). |
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workflows/lrsomatic.nf
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| ch_multiqc_files = ch_multiqc_files.mix(NANOPLOT_PRE.out.txt.collect{it -> it[1]}.ifEmpty([])) | ||
| ch_multiqc_files = ch_multiqc_files.mix(NANOPLOT_POST.out.txt.collect{it -> it[1]}.ifEmpty([])) | ||
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conf/modules.config
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| ext.prefix = { "${meta.id}_${meta.type}_ubam" } | ||
| publishDir = [ | ||
| path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_${meta.replicate}/" }, | ||
| path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam${meta.replicate}" }, |
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| path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_aln" }, | ||
| mode: params.publish_dir_mode, |
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
…lrsomatic into multiqc_nanoplot
robert-a-forsyth
approved these changes
Mar 13, 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).