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Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Update regex pattern for BED file path validation
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
coverage - filter seqcap genelists
only use first versions of modules
Workflow output definitions
* add mqc_sav module * fix bclconvert config * add demux logging * typo * fix rg function * fix rg function * catch library from sampleinfo if applicable * fix bclconvert meta.id * add cgroup metrics plugin * Remove nf-cgroup-metrics plugin from config * update multiqcsav and multiqc * mv rg function to lib * add mqcsav and fix plumbing * changelog * fix syntax error * Replace lib with function in subwf to please linter * update test config, fix issues * ditch conda from CI and update docs a little * fix file staging * fix linting * tinkering with configs * fix nf-test profiles * more work * linting * mqc_sav attempt #1 * Refactor MultiQC summary file handling and improve metadata management * fix test samplesheet * bump mqc_cmgg container * fix mqc output path * update modules + patch * fix multi-lane processing * fix SAV titleé * fix outputs and patch module * fix snap config process selector * set version to 3.0.0 * final fixed for multilane run qc (hopefully) * fix mqc inputs * move bclconvert rg function to subwf * fix final tests * let's hope we're done now... * fix main wf errors * fix tests (again) * test error * f*ck it * f*ck it
* bump modules * update subwf, include nf-teams * fix errors
* fix download test * Update parameters docs * Update output docs * drop conda profiles * update usage docs
nvnieuwk
approved these changes
Mar 6, 2026
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Major release featuring:
bclconvertoutput handlingalignerequalsfalse, withfalcoreportTODO before merging:
@nf-cmgg/core feel free to add ToDo's for features needed pre-audit