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Adding Picard tools for QC metrics
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Added optional Bwa index parameter to skip bwamem2 index for a faster output
Important! Template update for nf-core/tools v3.5.1
Co-authored-by: Pontus Höjer <pontus.hojer@scilifelab.se>
Validate test data
Pipeline description in README
Skip RUNDIRPARSER if no rundir information is available
Co-authored-by: Pontus Höjer <pontushojer@gmail.com>
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FriederikeHanssen
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Feb 12, 2026
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Just some minor comments. Double check the publishing please
* addess review comments * Update usage.md * Apply suggestion from @maxulysse * fix warning message about tag collision * CHANGELOG * Apply suggestion from @maxulysse * update contributor
FriederikeHanssen
approved these changes
Feb 16, 2026
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Make sure this ran through before clicking release: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2mFTkNnSIh6HVF/v2/tasks |
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It does work |
nvnieuwk
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Feb 17, 2026
nvnieuwk
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Feb 17, 2026
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One small comment but looking good otherwise 🥳
mashehu
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Feb 17, 2026
FriederikeHanssen
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Feb 17, 2026
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Going to block this so we can talk module binaries
* code polish * code polish * Set NFT_WORKDIR dynamically * simplify logic * no params in workflows * code polish * code polish + view -> subscribe * CHANGELOG
* update all modules and subworkflows * snapshot for subworkflows * fix conda setup * update more modules * no channel versions in qc_bam * no channel versions in qc_bam * update seqfu and picard
FriederikeHanssen
approved these changes
Feb 20, 2026
* Remove unused modules + move PREPARE_GENOME to root main.nf * Actually not using BOWTIE2 * CHANGELOG * snapshot * regenerate snapshot * auto-format * Apply suggestion from @maxulysse
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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).