add nf-test to gatk4/bedtointervallist - #3936 #5251
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…s added again (see nf-core#5251) (nf-core#5328) delete gatk4/bedtointervallist from pytest_modules.yml Co-authored-by: LE BARS Victor <Victor@ar155065.univ-rennes1.fr>
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* Try alternative strategy for extracting tags * Add check to prevent confirm pass if no tags present * Fix some names for GHA steps * Add fake change in fastp module * Add fake change in bam_sort_stats_samtools module * Add fake changes to pytest module and subworkflow * Add debug step * fixup * Got some variable names wrong... * Add subworkflows back to nf-tests * revert confirm-pass if statement * use JQ to separate modules and subworkflows * Fix quoting when parsing tags * coerce modules and subworkflows to lower case * Add specific linting checks to dependencies * Single vs double quotes again * Some more variable fixing * this might work * fixup * yet another fixup * Correct modules -> subworkflows * Fake change to pytest module * Correct dependency * One more time * More sorting stuff out * Update modules/nf-core/gunzip/tests/main.nf.test * Add fake change to module without nf-test so pytest ONLY is triggered * fixup incorrect variable * Switch to using self-hosted Docker profile * Add dependency checker from Carson Miller * fixup * fix(.github/python/find_changed_files.py): detect nf files less greedily 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. * Revert to directories instead of files for module tagging * Create optional returntype for Python script * Remove superfluous python cache * feat: replace custom python with reusable github action for detecting nf-test changes * Fix variable name in output paths * Switch to new parents dir syntax * prod to bump version of action * Update .github/workflows/test.yml * Update .github/workflows/test.yml * Exclude more subworkflows from Conda * Update .github/workflows/test.yml * Update .github/workflows/test.yml * QUILT nf-test and bamlist (#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 (#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 <khazen@bluestargenomics.com> * Add Demuxem (#5504) * 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 (#5521) Fix folder renaming * fix stubs salmon (#5517) * fix stubs * fix stub¨ * Update modules/nf-core/salmon/quant/main.nf --------- Co-authored-by: Lucpen <lucia.penaperez@hasta-login.local> Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> * Update mcquant: Added nf-test and meta.yml information (#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 (#5416) * Added repeatmodeler/builddatabase * Fixed version extraction * Now doing md5 check on stable db files * bump wisecondorx to v1.2.7 (#5523) * Add Freemuxlet to modules (#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 <xichwu@eu-login-30.euler.ethz.ch> Co-authored-by: wxicu <xichen.wu@hpc-build01.scidom.de> * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.2 (#5527) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Updating sentieon to 202308.02 (#5525) * Updating sentieon to 202308.02 * Fixing typo * Fix stale action (#5530) * ci: Try not setting the repo-token * ci: Run clean-up on dispatch * Changed tag from single quotes to double quotes (#5531) Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * [TYPO] Align commas (#5380) Align commas Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * GFFREAD: updated to 0.12.7, added meta and fasta input/output (#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 was added again (see #5251) (#5328) delete gatk4/bedtointervallist from pytest_modules.yml Co-authored-by: LE BARS Victor <Victor@ar155065.univ-rennes1.fr> * Update mosdepth to 0.3.8 (#5538) * Update mosdepth to 0.3.8 * Updating main.nf.test.snap * migrating flash to nf-test (#5470) * migrating flash to nf-test * removing args2 from main.nf * Update nextflow.config * Changes discussed in the outputs --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * add riboseq transcriptome bam to test config (#5537) * add ribo-seq transcriptome bam * remove extra line * Update nanoplot/main.nf (#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 (#5536) * repeatmodeler/repeatmodeler * Demoted to process_medium * Update modules/nf-core/repeatmodeler/repeatmodeler/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Blastdbcmd new module (#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 <jfy133@gmail.com> * Update modules/nf-core/blast/blastdbcmd/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <jfy133@gmail.com> * 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 <jfy133@gmail.com> --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Remove fake changes Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> * Use merge group base ref instead of PR base_ref when merging * fixup * Use SHA instead of head ref * fixup * work * origin/ * cmon * one more time with feeling * fixup again * Worth a try * Increase fetch depth to 2 * Use SHA instead of head ref --------- Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Kyle Hazen <41054023+k1sauce@users.noreply.github.com> Co-authored-by: Kyle <khazen@bluestargenomics.com> Co-authored-by: Mylène Mariana Gonzales André <103585173+mari-ga@users.noreply.github.com> Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> Co-authored-by: Lucía Peña-Pérez <lucia.pena.perez@scilifelab.se> Co-authored-by: Lucpen <lucia.penaperez@hasta-login.local> Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> Co-authored-by: Florian Wuennemann <flowuenne@gmail.com> Co-authored-by: Usman Rashid <usman@smme.edu.pk> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Xichen Wu <102925032+wxicu@users.noreply.github.com> Co-authored-by: Xichen Wu <xichwu@eu-login-30.euler.ethz.ch> Co-authored-by: wxicu <xichen.wu@hpc-build01.scidom.de> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Leon Hafner <60394289+LeonHafner@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Leon Rauschning <99650940+lrauschning@users.noreply.github.com> Co-authored-by: vlebars <104759956+vlebars@users.noreply.github.com> Co-authored-by: LE BARS Victor <Victor@ar155065.univ-rennes1.fr> Co-authored-by: DavideBag <96130443+DavideBag@users.noreply.github.com> Co-authored-by: iraiosub <48185776+iraiosub@users.noreply.github.com> Co-authored-by: Ashot Margaryan <9378723+ashotmarg@users.noreply.github.com> Co-authored-by: Toni Hermoso Pulido <toniher@cau.cat> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com>
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PR checklist
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda