portcullis/full: accommodate more outputs #8166
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* 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]>
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* 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]>
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* 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]>
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* 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]>
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PR checklist
Closes #8159
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