Update vrhyme modules, including nf-test #8163
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
SPPearce
changed the title
atrigila
reviewed
Apr 4, 2025
SPPearce
commented
Apr 4, 2025
SPPearce
added a commit
that referenced
this pull request
Apr 14, 2025
* Swap vrhyme/extractunbinned to nf-test * Swap linkbins to nf-test, add ontology, automatically gunzip * Fix linting * Update snapshot * Update modules/nf-core/vrhyme/vrhyme/meta.yml
github-merge-queue bot
pushed a commit
that referenced
this pull request
Apr 18, 2025
* Initial conversion, needs snapshots generating * Add tnscope * Update tnscope and tnhaplotyper2 * Remove ultra/index * Remove empty config * Reset pytest_modules * Fix meta * Reorder meta * Update modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test * Add env block * Update version for updateblastdb (#8181) * Change FastQC memory parameter from float to int (#8180) Removed call to toFloat, to keep memory value integral * updated bandage image to latest version (#8185) * portcullis/full: accommodate more outputs (#8166) * accommodate more outputs * Update main.nf * Update meta.yml * update nf-test assertions and snapshot * fix bam test --------- Co-authored-by: Anne Marie Noronha <[email protected]> Co-authored-by: Juan Blanco Heredia <[email protected]> * update freyja module to latest version (#8184) * updated freyja update to latest version * updated freyja variants to latest version * updated freyja boot to latest release * updated freyja demix to latest release * fix freyja update and variants with fixed bioconda recipe * updated snapshot for subworkflow after freyja update * fixed meta.yml for freyja update * correctly updated freyja boot container and snapshot * Update bcftools (#8182) * updated bcftools annotate to latest version * updated bcftools call to latest version * updated bcftools concat to latest version * updated bcftools consensus to latest version * updated bcftools convert to latest version * updated bcftools csq to latest version * updated bcftools filter to latest version * updated bcftools index to latest version * updated bcftools isec to latest version * updated bcftools merge to latest version * updated bcftools mpileup to latest version * updated bcftools norm to latest version * updated bcftools pluginimputeinfo to latest version * updated bcftools pluginscatter to latest version * updated bcftools pluginsplit to latest version * updated bcftools plugintag2tag to latest version * updated bcftools query latest version * updated reheader query latest version * updated roh query latest version * updated sort query latest version * updated split query latest version * updated stats query latest version * updated bcftools view latest version * updated snapshot for bam_ngscheck mate after bcftools update * added required tags to pass linting * fixed bam_ngscheckmate to pass linting * Fix bam_ngscheckmate --------- Co-authored-by: Simon Pearce <[email protected]> * updated artic to latest version (#8186) * Add functionality for `--unknown-slide` in `spaceranger/count` (#7233) * Add functionality for `--unknown-slide` option Add functionality to be able to use the `--unknown-slide` option of Space Ranger Count, specified using the `slide` column in the input samplesheet. * Fix tests snapshots for spaceranger/count * Update Docker image location and version * Update README with Docker image location / version * Add stubs for spaceranger/[mkref/mkgtf] * Minor formatting * Add stub code for spaceranger/mkgtf * Update spacreranger snapshots * Remove obsolete snapshots in spaceranger/counts * Fix snapshots * Update spaceranger/mkref snapshots * Add slide/area as inputs instead of meta values Add the slide and area values as module inputs instead of meta values (i.e. `meta.slide` and `meta.area`) as before, as this does not follow the module guidelines. Also update `meta.yml` and tests accordingly. * Fix erroneous test inputs * Ignore Dockerfile as module name * use uv & update filter pattern * fix syntax error * Revert "use uv & update filter pattern" This reverts commit f4daa56. * update subworkflow filter * Update .github/workflows/lint.yml Co-authored-by: Júlia Mir Pedrol <[email protected]> --------- Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Christophe Avenel <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> * Add threads parameter for all seqkit modules missing (#8192) Add threads for all seqkit modules missing (and language server autoformatting) * Support formula in `abundance_differential_filter` and associated modules (#8171) * refact: update structure of `variancepartition/dream` * refact: allow formula in channel inputs * docs: add formula to meta * fix: unstable digits in limma modules * Apply suggestions from code review Co-authored-by: Jonathan Manning <[email protected]> * refact: use formula in `variancepartition/dream` only * docs: remove meta example --------- Co-authored-by: Jonathan Manning <[email protected]> * Update shinyngs modules (#8194) * add module integronfinder (#8131) * add module integronfinder * I fix the issue of unstable snapshot * I fix the issue of identifier in meta.yml file * Update modules/nf-core/integronfinder/main.nf Co-authored-by: Louis Le Nézet <[email protected]> * I specify only the information about the version rather than the others and update the content of yml file * I remove the optional command arguments * update test to avoid unprintable char * I update the optional extention and fix mismatched hashes * I fixed the unbound variable error of CONDA_PREFIX * I fixed the unbound variable error of CONDA_PREFIX of stub * I update ontologies and remove snapshot content of files * I update the version.yml snapshot * I change the command for version extraction and modify the assert * I update the stub, the assert and fix the lint error * I update the assert snapshot for two outputs * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <[email protected]> * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <[email protected]> --------- Co-authored-by: Louis Le Nézet <[email protected]> * add gpu snapshot updater action (#8183) * add gpu snapshot updater action * remove sention * Update dependency python to 3.13 (#8189) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Mindagap stub and test updates (#8200) * updated mindagap stubs and tests * fix numpy version * fixed bug in bandage/image module, wrong versions.yml outputted (#8196) * fixed bug in bandage/image module, wrong versions.yml outputted * update fix just for versions generation * fix formatting in sylphtax/taxprof (#8202) Co-authored-by: Sofia Stamouli <[email protected]> * run update snapshot on gpu runners (#8201) * add nf-test and stub to svtk/standardize (#7768) * add nf-test and stub * gather caller info using meta * lint * update version * change conda version * remove tag from conda * update conda image * fix bad indentation * renew bioconda image * skip conda * skip conda in nf-test * fix typo in gpu-snapshot updater (#8204) fix typo * update vep to 113.4 and redo conda tests (#8205) * update vep to 113.4 and redo conda tests * also unskip vep subwf * Fix one more typo (#8207) * fix typo * fix one more typo in snapshot updater * change MUSE_SUMP to high memory module (#8212) * change MUSE_SUMP to high memory module * update version string * fix meta * change to avoid empty vcf * change version accession * upgrade muse call to process_high * upgrade muse sump to process_high * Update tj-actions/changed-files digest to 6cb76d0 (#8217) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix: PoolSNP: Update input tuple; cleanup stub (#8218) * Update input tuple; cleanup stub * Update meta.yml for poolsnp * Fix to rnaseq preprocessing linting fix (#8221) Fix to #7881 * Update modkit and porechop modules (#8223) * Update modkit and porechop modules * update link to porechop singularity container * update link --------- Co-authored-by: ra25wog <[email protected]> * Metaspace download (#8145) * Add metaspace/download module and fix issues from Bishoy's feedback(#8145) * added stub * change environment.yml bioconda::metaspace2020 --------- Co-authored-by: Bishoy Wadie <[email protected]> * Update vrhyme modules, including nf-test (#8163) * Swap vrhyme/extractunbinned to nf-test * Swap linkbins to nf-test, add ontology, automatically gunzip * Fix linting * Update snapshot * Update modules/nf-core/vrhyme/vrhyme/meta.yml * nf-test migration: cellrangerarc/count (#8008) * Begin migration for cellrangerarc/count * Tidy up whitespace * cellrangerarc/count full test working * Commiting broken stub test on purpose * Remove redundant config * Turn off Conda tests in CI * Add nextflow.config * Add single whitespace to add this file to CI tests * Revert "Add single whitespace to add this file to CI tests" This reverts commit 39b7f4c. * Revert "Revert "Add single whitespace to add this file to CI tests"" This reverts commit f65f635. --------- Co-authored-by: Sateesh_Peri <[email protected]> * Add sylphtax/merge and update taxprof to version 1.2 (#8228) * Clair3 (#7838) * Add use of prepackaged Clair3 models * Add dual input test and update screenshot * Update yaml * Update conda checking * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update nftest indentation * Update yml * Update tests and error handle --------- Co-authored-by: Felix Lenner <[email protected]> * update to doubled runner resources (#8233) * GTDBTK_CLASSIFYWF database improvement (#8220) * Add new input channel for premade seqid2map file * Add extra tests for using custom seqid2map file * Apply suggestions from code review * Update modules/nf-core/kraken2/build/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Make database supply to GTDBTK classify WF more robust * Fix metadata * Update modules/nf-core/gtdbtk/classifywf/meta.yml Co-authored-by: Jim Downie <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Jim Downie <[email protected]> * handle filtered out modules and subworkflow files in the linting step correctly (#8235) handle filtered out moudles and subworkflow files * fix linting check to run on files, not general changes (#8240) check to run on files, not general changes * always commit changes when run gpu-snapshot bot runs succesfully (#8237) always commit changes when run succesfully * Plink2 hwe (#8227) * Add plink2/filter * Update plink2/filter * add maf exit filter * edit maf * maf running update * Add new module plink2/maf * Add new module plink2/maf * Add plink2/maf module * Update modules/nf-core/plink2/maf/main.nf Co-authored-by: Simon Pearce <[email protected]> * Add plink2/maf module * Add plink2 HWE module * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/plink2/hwe/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * post review edit plink2 HWE module * edit plink2 HWE --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * migrate nf-test: survivor-filter (#8229) * migrate nf-test: survivor-filter * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * renew snapshot * remove stub snapshots * remove config --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * ragtag/scaffold and ragtag/patch modules and tests (#8198) * ragtag/scaffold and ragtag/patch modules and tests * more keywords in scaffold meta.yml * @jfy133 reviews * exclude some empty files from test snapshot * use modules_testdata_base_path in tests * more input channels * fix meta.ymls * disable error redirection in ragtag/patch * capture stdout * capture correctly * use symlinks instead of copying * logging for ragtag/scaffold * experimental: kill tail * experimental: kill tail * escape correctly --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * Nf-test migration survivor/simsv (#8251) * initial * renew snapshot * Stecfinder nftest (#8243) * Swap stecfinder to nf-test * Add stub, bump version * Fix mutect tests (#8242) * update mutect2 * update test & snap * nf-test migration: plink/indeppairwise (#8133) * Migrated pytest to nf-test for `plink/indeppairwise` module & added stub run and test to it. * Update modules/nf-core/plink/indeppairwise/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Fixed nf-test based on PR comments. * Restored `.pre-commit-config.yaml` to original state. * Update modules/nf-core/plink/indeppairwise/main.nf Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Uncomment logging. (#8248) * Swap shigeifinder to nf-test (#8245) * Swap to nf-test * Add setuptools to conda * Migrate `cellrangerarc/mkref`to nf-test (#8219) * Update to nf-test * Skip conda CI test * Correct mistake in pytest-workflow.yml * Update snapshot and add the suggestions --------- Co-authored-by: Famke Bäuerle <[email protected]> * Plink2 filter (#8247) * Add plink2/filter * Update plink2/filter * add module plink2 filter * edit module plink2 filter * update module plink2 filter * edit module plink2 filter * add more tests to plink2 filter * Use modules_testdata_base_path (#8259) fix path * nf-test + stub: svtk/rdtest2vcf (#8258) * nf-test + stub: svtk/rdtest2vcf * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/svtk/rdtest2vcf/main.nf Co-authored-by: Simon Pearce <[email protected]> * add tags * skip conda --------- Co-authored-by: Simon Pearce <[email protected]> * dragmap hashtable - snapshot versions (#8261) snapshot versions * Add gatk4/modelsegments (#8234) * gatk4/modelsegments module Fixes #8232. * Add tests * Fix tests * Address review comments Test do not work and I do not know why yet. * More review comments * More fixes wrt fomratting * More adjustments to the tests (still non-working) * Fix tests (at last!) * Remove redundant options * Rename args to be more descriptive * Re-update docker options * Update GTDB-TK: Update container version and fix a couple of error sources [do not merge - waiting on local test] (#8255) Update container version and fix a couple of error sources * Add custom adapters list as input argument (#8262) * Add custom adapters list as input argument * Update meta.yml and correct argument * Update GitHub Actions (#8253) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Migrate `GENOTYPHI_PARSE` to nf-test (#8265) Migrate to nf-test * Fix prettier porechop meta (#8266) * Fix errant bash comment in gtdbtk/classifywf (#8267) Update main.nf * Downgrade dragmap to the previous functionning version (#8263) * snapshot versions * downgrade dragmap to a working version * update tests and snapshots * improve tests + fix environment.yml * cursor :shakefist: * same warning text * fix linting * fix versions in environment.yml * update snapshots * channels * new module: fusioncatcher build (#8268) * add fusioncatcher build * fix linting * add a comment to test * new module: fusioncatcher/fusioncatcher (#8271) * Deprecate `FCS_FCSGX` (#8269) * Migrate to nf-test * Deprecate fcs * Set back code * Add failing test * Fix test * Fix test * Update comments --------- Co-authored-by: LouisLeNezet <[email protected]> * Migrate `gem2/gem2bedmappability` to nf-test (#8275) Migrate to nf-test Co-authored-by: LouisLeNezet <[email protected]> * Migrate `gem2/gemmappability` to nf-test (#8278) Migrate to nf-test Co-authored-by: LouisLeNezet <[email protected]> * Migrate `genescopefk` to nf-test (#8277) * Migrate to nf-test * Add parameters * Update modules/nf-core/genescopefk/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/genescopefk/main.nf Co-authored-by: Famke Bäuerle <[email protected]> --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * gatk4spark - better assertion and stub tests (#8274) * better assertion and stub tests * polish * capture versions better * fix paths * Links (#8260) * module without test * LINKS test * assert names of files that are not snapshotted * review comments * no zcat magic :( * more tests, switched to gzip instead of zcat * Migrate `damageprofiler` to nf-test (#8282) * Migrate to nf-test * Sort output --------- Co-authored-by: LouisLeNezet <[email protected]> * Bump genmod to 3.10 (#8281) * remove plink2 hwe (#8280) remove plink2 hwe * Update snapshots * Update snapshots * Update snapshots * Update tnscope * Add spaces and remove //meta * Update snapshots * Update modules/nf-core/sentieon/tnhaplotyper2/main.nf Co-authored-by: Louis Le Nézet <[email protected]> * Fix whitespace --------- Co-authored-by: Daniel Schmitz <[email protected]> Co-authored-by: Sara Monzón <[email protected]> Co-authored-by: Anne Marie Noronha <[email protected]> Co-authored-by: Anne Marie Noronha <[email protected]> Co-authored-by: Juan Blanco Heredia <[email protected]> Co-authored-by: Erik Fasterius <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Christophe Avenel <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: nguyent-son <[email protected]> Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <[email protected]> Co-authored-by: Sofia Stamouli <[email protected]> Co-authored-by: Kübra Narcı <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Abhilesh Dhawanjewar <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: Ding Yang Wang <[email protected]> Co-authored-by: Bishoy Wadie <[email protected]> Co-authored-by: ignatiusm <[email protected]> Co-authored-by: robert-a-forsyth <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Jim Downie <[email protected]> Co-authored-by: jodennehy <[email protected]> Co-authored-by: Niklas Schandry <[email protected]> Co-authored-by: Matias Perrone <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Maxime Laurent <[email protected]> Co-authored-by: Luca Beltrame <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Niklas Schandry <[email protected]>
famosab
pushed a commit
to famosab/modules
that referenced
this pull request
Jun 3, 2025
* Swap vrhyme/extractunbinned to nf-test * Swap linkbins to nf-test, add ontology, automatically gunzip * Fix linting * Update snapshot * Update modules/nf-core/vrhyme/vrhyme/meta.yml
famosab
added a commit
to famosab/modules
that referenced
this pull request
Jun 3, 2025
* Initial conversion, needs snapshots generating * Add tnscope * Update tnscope and tnhaplotyper2 * Remove ultra/index * Remove empty config * Reset pytest_modules * Fix meta * Reorder meta * Update modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test * Add env block * Update version for updateblastdb (nf-core#8181) * Change FastQC memory parameter from float to int (nf-core#8180) Removed call to toFloat, to keep memory value integral * updated bandage image to latest version (nf-core#8185) * portcullis/full: accommodate more outputs (nf-core#8166) * accommodate more outputs * Update main.nf * Update meta.yml * update nf-test assertions and snapshot * fix bam test --------- Co-authored-by: Anne Marie Noronha <[email protected]> Co-authored-by: Juan Blanco Heredia <[email protected]> * update freyja module to latest version (nf-core#8184) * updated freyja update to latest version * updated freyja variants to latest version * updated freyja boot to latest release * updated freyja demix to latest release * fix freyja update and variants with fixed bioconda recipe * updated snapshot for subworkflow after freyja update * fixed meta.yml for freyja update * correctly updated freyja boot container and snapshot * Update bcftools (nf-core#8182) * updated bcftools annotate to latest version * updated bcftools call to latest version * updated bcftools concat to latest version * updated bcftools consensus to latest version * updated bcftools convert to latest version * updated bcftools csq to latest version * updated bcftools filter to latest version * updated bcftools index to latest version * updated bcftools isec to latest version * updated bcftools merge to latest version * updated bcftools mpileup to latest version * updated bcftools norm to latest version * updated bcftools pluginimputeinfo to latest version * updated bcftools pluginscatter to latest version * updated bcftools pluginsplit to latest version * updated bcftools plugintag2tag to latest version * updated bcftools query latest version * updated reheader query latest version * updated roh query latest version * updated sort query latest version * updated split query latest version * updated stats query latest version * updated bcftools view latest version * updated snapshot for bam_ngscheck mate after bcftools update * added required tags to pass linting * fixed bam_ngscheckmate to pass linting * Fix bam_ngscheckmate --------- Co-authored-by: Simon Pearce <[email protected]> * updated artic to latest version (nf-core#8186) * Add functionality for `--unknown-slide` in `spaceranger/count` (nf-core#7233) * Add functionality for `--unknown-slide` option Add functionality to be able to use the `--unknown-slide` option of Space Ranger Count, specified using the `slide` column in the input samplesheet. * Fix tests snapshots for spaceranger/count * Update Docker image location and version * Update README with Docker image location / version * Add stubs for spaceranger/[mkref/mkgtf] * Minor formatting * Add stub code for spaceranger/mkgtf * Update spacreranger snapshots * Remove obsolete snapshots in spaceranger/counts * Fix snapshots * Update spaceranger/mkref snapshots * Add slide/area as inputs instead of meta values Add the slide and area values as module inputs instead of meta values (i.e. `meta.slide` and `meta.area`) as before, as this does not follow the module guidelines. Also update `meta.yml` and tests accordingly. * Fix erroneous test inputs * Ignore Dockerfile as module name * use uv & update filter pattern * fix syntax error * Revert "use uv & update filter pattern" This reverts commit f4daa56. * update subworkflow filter * Update .github/workflows/lint.yml Co-authored-by: Júlia Mir Pedrol <[email protected]> --------- Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Christophe Avenel <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> * Add threads parameter for all seqkit modules missing (nf-core#8192) Add threads for all seqkit modules missing (and language server autoformatting) * Support formula in `abundance_differential_filter` and associated modules (nf-core#8171) * refact: update structure of `variancepartition/dream` * refact: allow formula in channel inputs * docs: add formula to meta * fix: unstable digits in limma modules * Apply suggestions from code review Co-authored-by: Jonathan Manning <[email protected]> * refact: use formula in `variancepartition/dream` only * docs: remove meta example --------- Co-authored-by: Jonathan Manning <[email protected]> * Update shinyngs modules (nf-core#8194) * add module integronfinder (nf-core#8131) * add module integronfinder * I fix the issue of unstable snapshot * I fix the issue of identifier in meta.yml file * Update modules/nf-core/integronfinder/main.nf Co-authored-by: Louis Le Nézet <[email protected]> * I specify only the information about the version rather than the others and update the content of yml file * I remove the optional command arguments * update test to avoid unprintable char * I update the optional extention and fix mismatched hashes * I fixed the unbound variable error of CONDA_PREFIX * I fixed the unbound variable error of CONDA_PREFIX of stub * I update ontologies and remove snapshot content of files * I update the version.yml snapshot * I change the command for version extraction and modify the assert * I update the stub, the assert and fix the lint error * I update the assert snapshot for two outputs * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <[email protected]> * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <[email protected]> --------- Co-authored-by: Louis Le Nézet <[email protected]> * add gpu snapshot updater action (nf-core#8183) * add gpu snapshot updater action * remove sention * Update dependency python to 3.13 (nf-core#8189) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Mindagap stub and test updates (nf-core#8200) * updated mindagap stubs and tests * fix numpy version * fixed bug in bandage/image module, wrong versions.yml outputted (nf-core#8196) * fixed bug in bandage/image module, wrong versions.yml outputted * update fix just for versions generation * fix formatting in sylphtax/taxprof (nf-core#8202) Co-authored-by: Sofia Stamouli <[email protected]> * run update snapshot on gpu runners (nf-core#8201) * add nf-test and stub to svtk/standardize (nf-core#7768) * add nf-test and stub * gather caller info using meta * lint * update version * change conda version * remove tag from conda * update conda image * fix bad indentation * renew bioconda image * skip conda * skip conda in nf-test * fix typo in gpu-snapshot updater (nf-core#8204) fix typo * update vep to 113.4 and redo conda tests (nf-core#8205) * update vep to 113.4 and redo conda tests * also unskip vep subwf * Fix one more typo (nf-core#8207) * fix typo * fix one more typo in snapshot updater * change MUSE_SUMP to high memory module (nf-core#8212) * change MUSE_SUMP to high memory module * update version string * fix meta * change to avoid empty vcf * change version accession * upgrade muse call to process_high * upgrade muse sump to process_high * Update tj-actions/changed-files digest to 6cb76d0 (nf-core#8217) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix: PoolSNP: Update input tuple; cleanup stub (nf-core#8218) * Update input tuple; cleanup stub * Update meta.yml for poolsnp * Fix to rnaseq preprocessing linting fix (nf-core#8221) Fix to nf-core#7881 * Update modkit and porechop modules (nf-core#8223) * Update modkit and porechop modules * update link to porechop singularity container * update link --------- Co-authored-by: ra25wog <[email protected]> * Metaspace download (nf-core#8145) * Add metaspace/download module and fix issues from Bishoy's feedback(nf-core#8145) * added stub * change environment.yml bioconda::metaspace2020 --------- Co-authored-by: Bishoy Wadie <[email protected]> * Update vrhyme modules, including nf-test (nf-core#8163) * Swap vrhyme/extractunbinned to nf-test * Swap linkbins to nf-test, add ontology, automatically gunzip * Fix linting * Update snapshot * Update modules/nf-core/vrhyme/vrhyme/meta.yml * nf-test migration: cellrangerarc/count (nf-core#8008) * Begin migration for cellrangerarc/count * Tidy up whitespace * cellrangerarc/count full test working * Commiting broken stub test on purpose * Remove redundant config * Turn off Conda tests in CI * Add nextflow.config * Add single whitespace to add this file to CI tests * Revert "Add single whitespace to add this file to CI tests" This reverts commit 39b7f4c. * Revert "Revert "Add single whitespace to add this file to CI tests"" This reverts commit f65f635. --------- Co-authored-by: Sateesh_Peri <[email protected]> * Add sylphtax/merge and update taxprof to version 1.2 (nf-core#8228) * Clair3 (nf-core#7838) * Add use of prepackaged Clair3 models * Add dual input test and update screenshot * Update yaml * Update conda checking * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update nftest indentation * Update yml * Update tests and error handle --------- Co-authored-by: Felix Lenner <[email protected]> * update to doubled runner resources (nf-core#8233) * GTDBTK_CLASSIFYWF database improvement (nf-core#8220) * Add new input channel for premade seqid2map file * Add extra tests for using custom seqid2map file * Apply suggestions from code review * Update modules/nf-core/kraken2/build/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Make database supply to GTDBTK classify WF more robust * Fix metadata * Update modules/nf-core/gtdbtk/classifywf/meta.yml Co-authored-by: Jim Downie <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Jim Downie <[email protected]> * handle filtered out modules and subworkflow files in the linting step correctly (nf-core#8235) handle filtered out moudles and subworkflow files * fix linting check to run on files, not general changes (nf-core#8240) check to run on files, not general changes * always commit changes when run gpu-snapshot bot runs succesfully (nf-core#8237) always commit changes when run succesfully * Plink2 hwe (nf-core#8227) * Add plink2/filter * Update plink2/filter * add maf exit filter * edit maf * maf running update * Add new module plink2/maf * Add new module plink2/maf * Add plink2/maf module * Update modules/nf-core/plink2/maf/main.nf Co-authored-by: Simon Pearce <[email protected]> * Add plink2/maf module * Add plink2 HWE module * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/plink2/hwe/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * post review edit plink2 HWE module * edit plink2 HWE --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * migrate nf-test: survivor-filter (nf-core#8229) * migrate nf-test: survivor-filter * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * renew snapshot * remove stub snapshots * remove config --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * ragtag/scaffold and ragtag/patch modules and tests (nf-core#8198) * ragtag/scaffold and ragtag/patch modules and tests * more keywords in scaffold meta.yml * @jfy133 reviews * exclude some empty files from test snapshot * use modules_testdata_base_path in tests * more input channels * fix meta.ymls * disable error redirection in ragtag/patch * capture stdout * capture correctly * use symlinks instead of copying * logging for ragtag/scaffold * experimental: kill tail * experimental: kill tail * escape correctly --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * Nf-test migration survivor/simsv (nf-core#8251) * initial * renew snapshot * Stecfinder nftest (nf-core#8243) * Swap stecfinder to nf-test * Add stub, bump version * Fix mutect tests (nf-core#8242) * update mutect2 * update test & snap * nf-test migration: plink/indeppairwise (nf-core#8133) * Migrated pytest to nf-test for `plink/indeppairwise` module & added stub run and test to it. * Update modules/nf-core/plink/indeppairwise/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Fixed nf-test based on PR comments. * Restored `.pre-commit-config.yaml` to original state. * Update modules/nf-core/plink/indeppairwise/main.nf Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Uncomment logging. (nf-core#8248) * Swap shigeifinder to nf-test (nf-core#8245) * Swap to nf-test * Add setuptools to conda * Migrate `cellrangerarc/mkref`to nf-test (nf-core#8219) * Update to nf-test * Skip conda CI test * Correct mistake in pytest-workflow.yml * Update snapshot and add the suggestions --------- Co-authored-by: Famke Bäuerle <[email protected]> * Plink2 filter (nf-core#8247) * Add plink2/filter * Update plink2/filter * add module plink2 filter * edit module plink2 filter * update module plink2 filter * edit module plink2 filter * add more tests to plink2 filter * Use modules_testdata_base_path (nf-core#8259) fix path * nf-test + stub: svtk/rdtest2vcf (nf-core#8258) * nf-test + stub: svtk/rdtest2vcf * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/svtk/rdtest2vcf/main.nf Co-authored-by: Simon Pearce <[email protected]> * add tags * skip conda --------- Co-authored-by: Simon Pearce <[email protected]> * dragmap hashtable - snapshot versions (nf-core#8261) snapshot versions * Add gatk4/modelsegments (nf-core#8234) * gatk4/modelsegments module Fixes nf-core#8232. * Add tests * Fix tests * Address review comments Test do not work and I do not know why yet. * More review comments * More fixes wrt fomratting * More adjustments to the tests (still non-working) * Fix tests (at last!) * Remove redundant options * Rename args to be more descriptive * Re-update docker options * Update GTDB-TK: Update container version and fix a couple of error sources [do not merge - waiting on local test] (nf-core#8255) Update container version and fix a couple of error sources * Add custom adapters list as input argument (nf-core#8262) * Add custom adapters list as input argument * Update meta.yml and correct argument * Update GitHub Actions (nf-core#8253) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Migrate `GENOTYPHI_PARSE` to nf-test (nf-core#8265) Migrate to nf-test * Fix prettier porechop meta (nf-core#8266) * Fix errant bash comment in gtdbtk/classifywf (nf-core#8267) Update main.nf * Downgrade dragmap to the previous functionning version (nf-core#8263) * snapshot versions * downgrade dragmap to a working version * update tests and snapshots * improve tests + fix environment.yml * cursor :shakefist: * same warning text * fix linting * fix versions in environment.yml * update snapshots * channels * new module: fusioncatcher build (nf-core#8268) * add fusioncatcher build * fix linting * add a comment to test * new module: fusioncatcher/fusioncatcher (nf-core#8271) * Deprecate `FCS_FCSGX` (nf-core#8269) * Migrate to nf-test * Deprecate fcs * Set back code * Add failing test * Fix test * Fix test * Update comments --------- Co-authored-by: LouisLeNezet <[email protected]> * Migrate `gem2/gem2bedmappability` to nf-test (nf-core#8275) Migrate to nf-test Co-authored-by: LouisLeNezet <[email protected]> * Migrate `gem2/gemmappability` to nf-test (nf-core#8278) Migrate to nf-test Co-authored-by: LouisLeNezet <[email protected]> * Migrate `genescopefk` to nf-test (nf-core#8277) * Migrate to nf-test * Add parameters * Update modules/nf-core/genescopefk/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/genescopefk/main.nf Co-authored-by: Famke Bäuerle <[email protected]> --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * gatk4spark - better assertion and stub tests (nf-core#8274) * better assertion and stub tests * polish * capture versions better * fix paths * Links (nf-core#8260) * module without test * LINKS test * assert names of files that are not snapshotted * review comments * no zcat magic :( * more tests, switched to gzip instead of zcat * Migrate `damageprofiler` to nf-test (nf-core#8282) * Migrate to nf-test * Sort output --------- Co-authored-by: LouisLeNezet <[email protected]> * Bump genmod to 3.10 (nf-core#8281) * remove plink2 hwe (nf-core#8280) remove plink2 hwe * Update snapshots * Update snapshots * Update snapshots * Update tnscope * Add spaces and remove //meta * Update snapshots * Update modules/nf-core/sentieon/tnhaplotyper2/main.nf Co-authored-by: Louis Le Nézet <[email protected]> * Fix whitespace --------- Co-authored-by: Daniel Schmitz <[email protected]> Co-authored-by: Sara Monzón <[email protected]> Co-authored-by: Anne Marie Noronha <[email protected]> Co-authored-by: Anne Marie Noronha <[email protected]> Co-authored-by: Juan Blanco Heredia <[email protected]> Co-authored-by: Erik Fasterius <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Christophe Avenel <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: nguyent-son <[email protected]> Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <[email protected]> Co-authored-by: Sofia Stamouli <[email protected]> Co-authored-by: Kübra Narcı <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Abhilesh Dhawanjewar <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: Ding Yang Wang <[email protected]> Co-authored-by: Bishoy Wadie <[email protected]> Co-authored-by: ignatiusm <[email protected]> Co-authored-by: robert-a-forsyth <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Jim Downie <[email protected]> Co-authored-by: jodennehy <[email protected]> Co-authored-by: Niklas Schandry <[email protected]> Co-authored-by: Matias Perrone <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Maxime Laurent <[email protected]> Co-authored-by: Luca Beltrame <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Niklas Schandry <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.