feat: Add riboWaltz MultiQC custom content integration #139
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- Add ribowaltz_to_mqc.py script to transform riboWaltz TSV outputs to MultiQC custom content format (psite regions, frames, metaprofiles) - Create local RIBOWALTZ_MQC module to run the transform script - Create RIBOWALTZ_QC local subworkflow to encapsulate riboWaltz logic - Update riboWaltz module to export underlying data as TSV for all QC plots - Add riboWaltz to MultiQC top_modules for proper section ordering - Configure publishDir for riboWaltz outputs (QC to riboseq_qc/, coverage to other/) The MultiQC integration includes: - P-site region distribution bar chart with RNA-seq reference - Reading frame distribution grouped by transcript region - Metaprofile line graphs for start and stop codons 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
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Replace top_modules with numeric report_section_order to properly control the position of riboWaltz and other custom content sections in the MultiQC report.
Add report_section_order entries for preprocessing, alignment, and post-alignment QC sections so riboWaltz appears in the correct position (after alignment stats, before downstream analysis).
Add anchor properties to FastQC entries so they can be referenced by fastqc_raw and fastqc_trimmed in report_section_order.
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Example: multiqc_report.html |
iraiosub
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Jan 5, 2026
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LGTM - the multiQC report looks very neat! Feel free to merge after tests pass.
Simplify channel operations by using a single branch operator instead of three separate map/flatten/filter chains. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Extract common constants (PARENT_ID, PARENT_NAME, PARENT_DESC, REGIONS) - Add read_tsv_files() generator for DRY file reading - Add print_bargraph_header() helper for repeated YAML output - Simplify transform_metaprofile() using string formatting - Use dispatch dict instead of if/elif chain 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
The ribowaltz PDFs are published to riboseq_qc/ribowaltz/, not ribowaltz/. This covers both offset_plot/ and ribowaltz_qc/ subdirectories. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
PDF files are non-deterministic and should not be checksummed. The .nftignore already excludes them from future snapshots. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
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I'm closing this for now, we're going to make it a MultiQC plugin and avoid the complexity caused by the custom content |
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that sounds great! |
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Summary
ribowaltz_to_mqc.pyscript to transform riboWaltz TSV outputs to MultiQC custom content formatRIBOWALTZ_MQCmodule andRIBOWALTZ_QCsubworkflow to encapsulate riboWaltz logicriboseq_qc/, coverage toother/)The MultiQC integration includes:
Test plan
🤖 Generated with Claude Code