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* Back to dev 2.0.2dev * changelog * fix linting * Update CHANGELOG.md Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> --------- Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Template update for nf-core/tools version 3.2.1 * changelog * revert changes to README * revert asset changes * revert changes * revert changes * revert changes * revert more * revert * linting * linting
* Swap CI tests to nf-test * Changelog * fix linting * update snaps * update full snap * test csv * update csv * update snap * update full snap * update default snaps * update filter csv md5sum * change nxf veryion in ci * update test for instable variantsMD5 * update full snap * add filter conf back * linting * template * update snap * update snaps with fixed seed * rerun with singularity * update filter * update default * set removeIDs and rename flags explicitely to true * update test config * fix bcftools annotate output to hopefully fix failing tests * remove tbi output * update snaps * Update CHANGELOG.md * fix changelog headers * change order of snaps * default snap * remove nft-bam because its not used * check if fix solved instable vcf * Update nftignore etc * correct full snap * change normal and stub test order
* Update alle nf-core modules * changelog * correct snap * Dependencies
* Template update to version 3.3.1 * revert wrong changes * revert wrong changes * revert wrong changes * revert wrong changes * prettier * try linting fix * prettierignore * prettierignore * final line * fix linting finally * update multiqc * revert changes to nf-test action to check if diffs show again * revert changes to action * fix nf-test action * update snaps * change snapshot order * remove .parquet md5sum
* Fix output of filtering module to avoid overwriting * Changelog * revert wrong change * change snap order * change snap order * fix linting * make sample and labels more meaningful for tests * Change order of test snaps * update output docs * Apply suggestions from code review * Update docs/output.md * Apply suggestions from code review * Update docs/output.md
* first steps * do it all in main workflow * finalize * nicer snap * nicer snap * move output * changelog * Update docs * Update docs/output.md Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * Apply suggestions from code review --------- Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
* Template update for nf-core/tools version 3.3.2 * update changelog * update changelog * fix readme * rocrate * readme * rocrate
* Template update for nf-core/tools version 3.3.2 * Template update for nf-core/tools version 3.5.1 * revert module removal * language server * fix some mistakes * some linting * rocrate * fix input schema * nextflow lint * pre-commit * update snaps * two small changes
* Template update for nf-core/tools version 4.0.2 * Revert a few changes * Fix linting * Fix input schema * Fix input schema * Fix linting * Update snaps * Update full snap
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Swap to https://killercup.github.io/codenamer/ and use SI Units + Colors (Extended) |
* Update all modules * Update filter snap * Remove test folders * swap to topics * fix linting
* Bump version * Update Changelog * Update CHANGELOG.md Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> --------- Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
d4straub
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May 20, 2026
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The code looks fine to me, but it was a little much and I might have missed something.
I think the download test should not be executed, I hope when this is merged it will be resolved. Otherwise it would be good to tackle that to make sure tests are meaningful.
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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).