Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow #9559
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…dness Pass BBSplit stats output to MultiQC for visualization of read binning statistics. MultiQC 1.33+ includes support for parsing BBSplit stats.txt files and displaying per-sample read distribution across reference genomes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
| BBMAP_BBSPLIT.out.primary_fastq.set { ch_filtered_reads } | ||
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| ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions.first()) | ||
| ch_multiqc_files = ch_multiqc_files.mix(BBMAP_BBSPLIT.out.stats) |
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are you stripping the meta later? I ran into that on sarek when adding it here
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FriederikeHanssen
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Dec 11, 2025
vagkaratzas
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Dec 12, 2025
…subworkflow (#9559) Add BBSplit stats to MultiQC files in fastq_qc_trim_filter_setstrandedness Pass BBSplit stats output to MultiQC for visualization of read binning statistics. MultiQC 1.33+ includes support for parsing BBSplit stats.txt files and displaying per-sample read distribution across reference genomes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]>
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PR checklist
Description of changes
This PR adds BBSplit statistics to the MultiQC output in the
fastq_qc_trim_filter_setstrandednesssubworkflow.Changes
BBMAP_BBSPLIT.out.statsto thech_multiqc_fileschannelWhy
MultiQC 1.33 introduced support for parsing BBSplit
stats.txtfiles, allowing visualization of:This provides users with an overview of reads removed during contaminant filtering.
Related
🤖 Generated with Claude Code