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* Template update for nf-core/tools version 3.4.1 * Template update for nf-core/tools version 3.4.1 * move params * changelog * Drocrate * snap * contriv * Apply suggestion from @maxulysse Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * Apply suggestion from @maxulysse Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * disable tower * skip fastqc * skip fastqc * snap --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Remove fastqc * Run pre-commit --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
* Add citations * Run pre-commit * Update CITATIONS.md Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
* Get PCGR reference automatically * change containers * add pcgr/getref * add pcgr/getref * update module inputs * add download * handle vep cahce * pre-commit * use nf-core module * cleanup * remove unused module * test * add snap for swbf and remove unused conf * adjust test memory limit * Update schema * change config * try using other genome for test * hard code genome to test * hard code genome to test * try cache from raredisease * try with untar * revert change to samplesheet * sawp * use NCBI igenome * swap to GATK * swap to GATK * Add VEP Cache for chr22 * current state * it workds * Add vep cache * rescue versions * update snap * use downsampled PCGR * fix linting * Add vcf assertion
* Add citations * Run pre-commit * Update CITATIONS.md Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Add test utils and default test * Apply suggestions from code review * Apply suggestion from @famosab * Apply suggestion from @famosab * Apply suggestion from @famosab --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Retrieve PCGR db and VEP cache automatically
* Template update for nf-core/tools version 3.4.1 * Template update for nf-core/tools version 3.5.1 * Template update for nf-core/tools version 3.5.1 * Small fixes * Update changelog * run nextflow lint * Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestions from code review --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Move test data to repo and add full_size test config * Changelog * Add full_size snap and tag for CI-tests * Apply suggestion from @famosab
* More changes to adhere to strict syntax * syntax * fix one more error * bump schema * bump schema
* Recover help message * changelog
Expand and adapt documentation
Joon-Klaps
reviewed
Mar 13, 2026
Joon-Klaps
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Joon-Klaps
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Very nice work on the conversion! A couple of things, I believe we can improve on.
* Rename subworkflow and add meta * alignment
11 tasks
* Fix typos and version * remove email template
* Add tests and meta to pcgr/preparevcf * add snap files to prettier ignore * add ci tag * revert prepare somatic change * fix snap * add tag * update reference data test * Add licenses and modify module * Update meta
* Add meta and tests to reformat modules * precommit * Add param * Update snaps * assert vcf correctly * Update snapshot
* First steps * Add tests * Update snap * correct more snaps * Apply suggestion from @famosab * use correct file * correct cna handling
* Add meta and tests to intersect/vcf * update reference meta * Update snap * Update isec again * recover pcgr * restore * update key file * Update snapshot * try sorting * update full snap * update intersect snap * Apply suggestions from code review from @Joon-Klaps Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Joon-Klaps
approved these changes
Mar 26, 2026
* Address review comments * fix refs
…vcf-file Make Mutect2 FORMAT detection flexible (allow optional FAD)
* update README.md * minor corrections * Update README.md Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update README.md Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: youssef.abili <youssef.abili@fht.org> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
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@maxulysse I think we need your review now on this real PR |
11 tasks
famosab
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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).