Fix 'multiqc_title' param modifying the output multiqc directory structure - #265
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pontushojer wants to merge 2 commits into
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Fix 'multiqc_title' param modifying the output multiqc directory structure#265pontushojer wants to merge 2 commits into
pontushojer wants to merge 2 commits into
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…reaking the report index section ([nf-core#261](nf-core#261))
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Pull request overview
This PR addresses nf-core/seqinspector issue #261 by ensuring that using --multiqc_title does not alter MultiQC output filenames and directories, which would otherwise break the report index links.
Changes:
- Pin MultiQC output names (
multiqc_report.html,multiqc_data,multiqc_plots) inassets/multiqc_config.ymlso they stay stable even when--multiqc_titleis set. - Add a changelog entry documenting the fix and linking the relevant issue and PR.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
assets/multiqc_config.yml |
Forces static MultiQC output filenames and directory names to prevent --multiqc_title from changing output structure. |
CHANGELOG.md |
Documents the fix and links to the relevant PR and issue. |
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| # Set static output file names for the report, data and plots directories so these | ||
| # are not changed when "--multiqc_title" is specified, required for index section to work properly | ||
| output_fn_name: "multiqc_report.html" | ||
| data_dir_name: "multiqc_data" | ||
| plots_dir_name: "multiqc_plots" |
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fix #261
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).