Try alternative strategy for extracting tags #4928
Commits on Feb 15, 2024
Commits on Apr 5, 2024
Commits on Apr 9, 2024
Commits on Apr 11, 2024
-
-
-
fix(.github/python/find_changed_files.py): detect nf files less greed…
…ily and ignore tests directory The scanning function was picking up nf files outside of the target repos. This change only scans modules, subworkflows and workflows.
-
-
-
-
Commits on Apr 15, 2024
-
feat: replace custom python with reusable github action for detecting…
… nf-test changes
-
-
-
-
Commits on Apr 16, 2024
Commits on Apr 30, 2024
-
QUILT nf-test and bamlist (nf-core#5515)
* Migrate quilt to nf-test and swithc bamlist to auto generation inside the module * Fix tests * Fix test * Fix tests * Add snap * Update license * Add quilt tag * Specify build hash for conda environment * Specify build hash for conda environment * Undo commit * Update nf-test snapshot * Fix config name * Update snapshot * Update meta.yml * Add r-base to environment * Update snapshot generation * Update meta.yml * Update snap * Update snap * Force sorting * Update snapshot
-
New module: gnu/split (nf-core#5428)
* dev * dev * dev * add tests * fix lint * fix(gnu/split): pin coreutils in conda to match singularity and docker * fix: minor formatting fixes, use modules_testdata_base_path in nf-test --------- Co-authored-by: Kyle <[email protected]>
-
* Fix lint test * added input * inputs and outputs demuxem * updates demuxem, missing snap test * fixes * out new parameters testing * tests passed * lint test check * editorconfig fixes * more fixes editorconfig * fix editorconfig * line 24 whitespace * blank spaces * fix line 23 * test to fix trailing whitespace * fix line23 * fix main
-
Fix AMRFinderPlus (nf-core#5521)
Fix folder renaming
-
fix stubs salmon (nf-core#5517)
* fix stubs * fix stub¨ * Update modules/nf-core/salmon/quant/main.nf --------- Co-authored-by: Lucpen <[email protected]> Co-authored-by: Annick Renevey <[email protected]>
-
Update mcquant: Added nf-test and meta.yml information (nf-core#5507)
* Transition to nf-test and meta.yml info fix. * Added MIT license. * Removed conda environment.yml for mcquant. * Added conda exclusion for nf-test. * Changed to quay.io container. * Removed quay.io from container
-
Added repeatmodeler/builddatabase (nf-core#5416)
* Added repeatmodeler/builddatabase * Fixed version extraction * Now doing md5 check on stable db files
-
-
Add Freemuxlet to modules (nf-core#5520)
* add freemuxlet * add snapshot * pass container test * remove trailing whitespace * add optional output files creation * remove ldist * fix test * add snapshot --------- Co-authored-by: Xichen Wu <[email protected]> Co-authored-by: wxicu <[email protected]>
-
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4…
….2 (nf-core#5527) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
-
Updating sentieon to 202308.02 (nf-core#5525)
* Updating sentieon to 202308.02 * Fixing typo
-
Fix stale action (nf-core#5530)
* ci: Try not setting the repo-token * ci: Run clean-up on dispatch
-
Changed tag from single quotes to double quotes (nf-core#5531)
Co-authored-by: Simon Pearce <[email protected]>
-
[TYPO] Align commas (nf-core#5380)
Align commas Co-authored-by: Simon Pearce <[email protected]>
-
GFFREAD: updated to 0.12.7, added meta and fasta input/output (nf-cor…
…e#5448) * GFFREAD: updated to 0.12.7, added meta and fasta input/output * Added a comment explaining args_sorted
-
re delete gatk4/bedtointervallist from pytest_modules.yml after it wa…
…s added again (see nf-core#5251) (nf-core#5328) delete gatk4/bedtointervallist from pytest_modules.yml Co-authored-by: LE BARS Victor <[email protected]>
-
Update mosdepth to 0.3.8 (nf-core#5538)
* Update mosdepth to 0.3.8 * Updating main.nf.test.snap
-
migrating flash to nf-test (nf-core#5470)
* migrating flash to nf-test * removing args2 from main.nf * Update nextflow.config * Changes discussed in the outputs --------- Co-authored-by: Simon Pearce <[email protected]>
-
add riboseq transcriptome bam to test config (nf-core#5537)
* add ribo-seq transcriptome bam * remove extra line
-
Update nanoplot/main.nf (nf-core#5460)
Update main.nf Updated the "def input_file" section so that it not only takes fastq file with ".fastq.gz" suffix but also ".fq.gz".
-
Added repeatmodeler/repeatmodeler (nf-core#5536)
* repeatmodeler/repeatmodeler * Demoted to process_medium * Update modules/nf-core/repeatmodeler/repeatmodeler/main.nf Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]>
-
Blastdbcmd new module (nf-core#5482)
* starting blastdbcmd * carry on * Making it work with simple entry version * Upgrade to make entry_batch work * Upgrade to make it work with tests * adding missing tag * Removed versions to make it pass the tests in Github * Make it work with versions and so * Update modules/nf-core/blast/blastdbcmd/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/blast/blastdbcmd/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> * Move module into two and upgrade according to comments * upgrade with outfmt forced * Turn back into one module * Update modules/nf-core/blast/blastdbcmd/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * update tags and stub test * fix stub * making it work more widely * editorcheck error * addressing comments * Update modules/nf-core/blast/blastdbcmd/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> --------- Co-authored-by: James A. Fellows Yates <[email protected]>
-
-
Co-authored-by: Carson J Miller <[email protected]>
