Fix rnaseq preprocessing: don't trim with bad linting by pinin4fjords · Pull Request #7881 · nf-core/modules

pinin4fjords · 2025-03-21T14:40:55Z

Just fixing a channel name to create the blocking from bad linting I'd intended when writing this.

PR checklist

Closes #XXX

itrujnara

Okay

pinin4fjords · 2025-03-21T15:06:56Z

Thanks!

* Module for PCA * Module for PCA * Module for PCA * Module for PCA * Module for PCA * testing conda * plinkpca * Fixed ivar modules (#7868) * fixed ivar variants module * updated snapshot ivar variants because versions change * fixed ivar consensus module * simplified snapshot for consensus test, same as ivar variants module * simplified snapshot for trim test, same as ivar variants module * updated snapshot for ivar trim and consensus modules * removed empty log file in ivar trim in snapshot * updated ivar version to last one * updated version also in conda env * updated version also in conda env in ivar consensus and variants * updated container version for ivar consensus and variants * updated snapshots again * Update FastK + MerquryFK versions + allow conda, add merquryfk/hapmaker module, port to nf-test (#7847) * Start updating FastK modules to allow conda * Migrate all Merquryfk modules to nf-test * Update to container with explicit R * Fix container for FastK * Start fixing fastk modules * Fix FastK tests, add merquryfk/hapmaker module * Fix linting for some merquryFK modules * Fix merquryfk/merquryfk linting * Fix linting for everything except hapmaker * Fix snapshots? * Update tests * Fix tests pt 1000 * Sort fastk/merge test inputs to try and ensure repeatability * Rename output channels to avoid linting error * Fix hapmaker snapshot * Harshill alignment * Stub output format determined by args; add details to meta.yml files to disambiguate meta maps * Remove def again from variables - causes error otherwise * Fix Fastk/merge stub * Update snapshot * Fix rnaseq preprocessing: don't trim with bad linting (#7881) * Update versions for motus/preplong (#7854) * Update versions for motus preplong * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> * Versions * Add tests for downloaddb * Add snapshot * Update to the latest motus merge * Update motus merge * Remove pytest * Update pytest * Update downloaddb * Update modules/nf-core/motus/downloaddb/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add stub * Add stub --------- Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fixed conda channel order for fq module (#7871) (#7873) * Fixed conda channel order for fq module (#7871) By listing bioconda as the primary channel, the fq package can be installed and used in conda environments. modified: modules/nf-core/fq/generate/environment.yml modified: modules/nf-core/fq/lint/environment.yml modified: modules/nf-core/fq/subsample/environment.yml * added channel order comment to avoid a regression --------- Co-authored-by: Angel Pizarro <pizarroa@amazon.com> * New module: `khmer/trimlowabund` (#7806) * add khmer/trimlowabund * use evironment.yml * chore(deps): update tj-actions/changed-files action to v46 (#7809) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added coreograph nf-test (#7812) coreograph nf-test * Added ilastik/multicut nftest (#7811) * main.nf changes * finished test * Update `graphtyper/vcfconcatenate`: Add batching to avoid long command line error (#7805) add batching to vcfconcatenate to avoid long command line error Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> * basicpy nf-test (#7772) * basicpy nf-test * removed leftover pytest * separate output files * updated meta * separated outputs * adapted test * adapted inputs and snapshot * removed pytest files --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Clair3 (#7765) * Adds Clair3 * Removes TODOs and changes container urls * Changes bash command * Removes useless code lines * Removes TODO statements * Update meta.yml adds more file info to meta.yml * Update main.nf.test removes TODO and updates clair3 model directory * Update meta.yml fixes doi link * Add suggestions and changes data pulling * Fix main.nf.test adds correct structure to pass data to main * fix yaml * fix yaml final one * Update test snapshot * Fix snapshot * Fix tests * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Change meta description * Update meta * Update meta * update screenshot * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * chore(deps): update github actions (#7796) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Change file name for severus_somatic.vcf (#7814) * Change file name for severus_somatic.vcf * Update snapshot * Update yaml * Clean up hifiasm module + add bin file input (#7802) * Tidy hifiasm model + update tests * Update nf.test * Fix linting * Add fasta and PAF outputs to hifiasm; combine all bin files into a single output channel. Update documentation * Improve descriptiveness of output channel names * fix samtools/convert stub (#7816) * add default memory if task.memory is not set * Update modules/nf-core/khmer/trimlowabund/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/khmer/trimlowabund/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update `sourmash/compare`: Name output by prefix and update conda/docker (#7808) * update sourmash/compare so output is named by prefix * add stub to sourmash/sketch * Update modules/nf-core/sourmash/sketch/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * move test for sourmash/gather from pytest to nf-test * migrated sourmash taxannotate to nf-test --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * add Subworkflow linting step to CI (#7835) add swf linting step * Add missing swf change detection (#7836) * add swf linting step * add missing change detection for subworkflows * Add bedtools/shuffle module (#7803) * Add bedtools/shuffle module * Make linter happy * Update test snapshots for bedtools/shuffle * add new ARCHIVE_EXTRACT subworkflow (#7817) * add new subworkflow * rename * fix tags * add basic meta.yml * better comments * Update subworkflows/nf-core/archive_extract/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * APPLYBQSR output line specificity (#7818) * updated output line and snap file * linting fix in meta * Trying out RunsOn runners (#7840) * Trying out RunsOn runners * try older image * add debugging * fix action * pin setup-apptainer * add gpu test * fix usage syntax * switch from docker_self_hosted to docker * remove test comments * Fix language server error in salmon/quant (#7843) * New module: `busco/download` (#7788) * add busco/download * add author/maintainer * update tests snap for new conda version * revert to older conda version to match container versions * update tests * add stub * removed unneeded code in stub --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> * Fix language server errors in arriba/arriba (#7845) * name output by prefix * set to process_medium * check if input and output file are the same * make sure regex matches only part of string * Update modules/nf-core/khmer/trimlowabund/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/khmer/trimlowabund/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * apply changes made to file path handeling to stub * Update modules/nf-core/khmer/trimlowabund/meta.yml * Update modules/nf-core/khmer/trimlowabund/meta.yml --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: John Orgera <65687576+johnoooh@users.noreply.github.com> * Added cram output to samtools/fixmate (#7820) * Added cram output to samtools/fixmate * Fixed tag * Fixed tag * Fixed linting * Updated onts * Use nft-bam, update output glob * Fixed meta.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Migrate `ATAQV/MKARV` to nf-test (#7893) Migrate to nf-test Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Added repeatmasker/repeatmasker (#7825) * Added repeatmasker/repeatmasker * Added onts * Added mdust (#7823) * Added mdust * Responded to review * Added agat/spfilterbyorfsize (#7822) * Added agat/spfilterbyorfsize * Added Gff tests * Migrate `authentict/deam2cont` to nf-test (#7947) * Update to nf-test * Fix samtools version * Update modules/nf-core/authentict/deam2cont/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/authentict/deam2cont/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/authentict/deam2cont/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Migrate `BAMTOOLS/CONVERT` to nf-test (#7958) * Migrate to nf-test * Update modules/nf-core/bamtools/convert/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update variable names * Fix spacing --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated deevariant to avoid failing nf-test (#7960) Updated the main to avoid failing nf-test * answer review Edo * fixing logfile * fixing variable name bug * rebasing * fixing variable name bug * fixing variable name bug --------- Co-authored-by: Bruno Ariano <bruno.ariano@fht.org> Co-authored-by: Sara Monzón <sara.monzon.fdz@gmail.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Angel Pizarro <delagoya@gmail.com> Co-authored-by: Angel Pizarro <pizarroa@amazon.com> Co-authored-by: Zachary Foster <zacharyfoster1989@gmail.com> Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: John Orgera <65687576+johnoooh@users.noreply.github.com> Co-authored-by: Usman Rashid <usman@smme.edu.pk> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Solenne Correard <54953390+scorreard@users.noreply.github.com>

* Module for PCA * Module for PCA * Module for PCA * Module for PCA * Module for PCA * testing conda * plinkpca * Fixed ivar modules (nf-core#7868) * fixed ivar variants module * updated snapshot ivar variants because versions change * fixed ivar consensus module * simplified snapshot for consensus test, same as ivar variants module * simplified snapshot for trim test, same as ivar variants module * updated snapshot for ivar trim and consensus modules * removed empty log file in ivar trim in snapshot * updated ivar version to last one * updated version also in conda env * updated version also in conda env in ivar consensus and variants * updated container version for ivar consensus and variants * updated snapshots again * Update FastK + MerquryFK versions + allow conda, add merquryfk/hapmaker module, port to nf-test (nf-core#7847) * Start updating FastK modules to allow conda * Migrate all Merquryfk modules to nf-test * Update to container with explicit R * Fix container for FastK * Start fixing fastk modules * Fix FastK tests, add merquryfk/hapmaker module * Fix linting for some merquryFK modules * Fix merquryfk/merquryfk linting * Fix linting for everything except hapmaker * Fix snapshots? * Update tests * Fix tests pt 1000 * Sort fastk/merge test inputs to try and ensure repeatability * Rename output channels to avoid linting error * Fix hapmaker snapshot * Harshill alignment * Stub output format determined by args; add details to meta.yml files to disambiguate meta maps * Remove def again from variables - causes error otherwise * Fix Fastk/merge stub * Update snapshot * Fix rnaseq preprocessing: don't trim with bad linting (nf-core#7881) * Update versions for motus/preplong (nf-core#7854) * Update versions for motus preplong * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> * Versions * Add tests for downloaddb * Add snapshot * Update to the latest motus merge * Update motus merge * Remove pytest * Update pytest * Update downloaddb * Update modules/nf-core/motus/downloaddb/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add stub * Add stub --------- Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fixed conda channel order for fq module (nf-core#7871) (nf-core#7873) * Fixed conda channel order for fq module (nf-core#7871) By listing bioconda as the primary channel, the fq package can be installed and used in conda environments. modified: modules/nf-core/fq/generate/environment.yml modified: modules/nf-core/fq/lint/environment.yml modified: modules/nf-core/fq/subsample/environment.yml * added channel order comment to avoid a regression --------- Co-authored-by: Angel Pizarro <pizarroa@amazon.com> * New module: `khmer/trimlowabund` (nf-core#7806) * add khmer/trimlowabund * use evironment.yml * chore(deps): update tj-actions/changed-files action to v46 (nf-core#7809) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added coreograph nf-test (nf-core#7812) coreograph nf-test * Added ilastik/multicut nftest (nf-core#7811) * main.nf changes * finished test * Update `graphtyper/vcfconcatenate`: Add batching to avoid long command line error (nf-core#7805) add batching to vcfconcatenate to avoid long command line error Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> * basicpy nf-test (nf-core#7772) * basicpy nf-test * removed leftover pytest * separate output files * updated meta * separated outputs * adapted test * adapted inputs and snapshot * removed pytest files --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Clair3 (nf-core#7765) * Adds Clair3 * Removes TODOs and changes container urls * Changes bash command * Removes useless code lines * Removes TODO statements * Update meta.yml adds more file info to meta.yml * Update main.nf.test removes TODO and updates clair3 model directory * Update meta.yml fixes doi link * Add suggestions and changes data pulling * Fix main.nf.test adds correct structure to pass data to main * fix yaml * fix yaml final one * Update test snapshot * Fix snapshot * Fix tests * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Change meta description * Update meta * Update meta * update screenshot * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * chore(deps): update github actions (nf-core#7796) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Change file name for severus_somatic.vcf (nf-core#7814) * Change file name for severus_somatic.vcf * Update snapshot * Update yaml * Clean up hifiasm module + add bin file input (nf-core#7802) * Tidy hifiasm model + update tests * Update nf.test * Fix linting * Add fasta and PAF outputs to hifiasm; combine all bin files into a single output channel. Update documentation * Improve descriptiveness of output channel names * fix samtools/convert stub (nf-core#7816) * add default memory if task.memory is not set * Update modules/nf-core/khmer/trimlowabund/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/khmer/trimlowabund/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update `sourmash/compare`: Name output by prefix and update conda/docker (nf-core#7808) * update sourmash/compare so output is named by prefix * add stub to sourmash/sketch * Update modules/nf-core/sourmash/sketch/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * move test for sourmash/gather from pytest to nf-test * migrated sourmash taxannotate to nf-test --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * add Subworkflow linting step to CI (nf-core#7835) add swf linting step * Add missing swf change detection (nf-core#7836) * add swf linting step * add missing change detection for subworkflows * Add bedtools/shuffle module (nf-core#7803) * Add bedtools/shuffle module * Make linter happy * Update test snapshots for bedtools/shuffle * add new ARCHIVE_EXTRACT subworkflow (nf-core#7817) * add new subworkflow * rename * fix tags * add basic meta.yml * better comments * Update subworkflows/nf-core/archive_extract/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * APPLYBQSR output line specificity (nf-core#7818) * updated output line and snap file * linting fix in meta * Trying out RunsOn runners (nf-core#7840) * Trying out RunsOn runners * try older image * add debugging * fix action * pin setup-apptainer * add gpu test * fix usage syntax * switch from docker_self_hosted to docker * remove test comments * Fix language server error in salmon/quant (nf-core#7843) * New module: `busco/download` (nf-core#7788) * add busco/download * add author/maintainer * update tests snap for new conda version * revert to older conda version to match container versions * update tests * add stub * removed unneeded code in stub --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> * Fix language server errors in arriba/arriba (nf-core#7845) * name output by prefix * set to process_medium * check if input and output file are the same * make sure regex matches only part of string * Update modules/nf-core/khmer/trimlowabund/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/khmer/trimlowabund/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * apply changes made to file path handeling to stub * Update modules/nf-core/khmer/trimlowabund/meta.yml * Update modules/nf-core/khmer/trimlowabund/meta.yml --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: John Orgera <65687576+johnoooh@users.noreply.github.com> * Added cram output to samtools/fixmate (nf-core#7820) * Added cram output to samtools/fixmate * Fixed tag * Fixed tag * Fixed linting * Updated onts * Use nft-bam, update output glob * Fixed meta.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Migrate `ATAQV/MKARV` to nf-test (nf-core#7893) Migrate to nf-test Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Added repeatmasker/repeatmasker (nf-core#7825) * Added repeatmasker/repeatmasker * Added onts * Added mdust (nf-core#7823) * Added mdust * Responded to review * Added agat/spfilterbyorfsize (nf-core#7822) * Added agat/spfilterbyorfsize * Added Gff tests * Migrate `authentict/deam2cont` to nf-test (nf-core#7947) * Update to nf-test * Fix samtools version * Update modules/nf-core/authentict/deam2cont/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/authentict/deam2cont/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/authentict/deam2cont/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Migrate `BAMTOOLS/CONVERT` to nf-test (nf-core#7958) * Migrate to nf-test * Update modules/nf-core/bamtools/convert/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update variable names * Fix spacing --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated deevariant to avoid failing nf-test (nf-core#7960) Updated the main to avoid failing nf-test * answer review Edo * fixing logfile * fixing variable name bug * rebasing * fixing variable name bug * fixing variable name bug --------- Co-authored-by: Bruno Ariano <bruno.ariano@fht.org> Co-authored-by: Sara Monzón <sara.monzon.fdz@gmail.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Angel Pizarro <delagoya@gmail.com> Co-authored-by: Angel Pizarro <pizarroa@amazon.com> Co-authored-by: Zachary Foster <zacharyfoster1989@gmail.com> Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: John Orgera <65687576+johnoooh@users.noreply.github.com> Co-authored-by: Usman Rashid <usman@smme.edu.pk> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Solenne Correard <54953390+scorreard@users.noreply.github.com>

Fix to #7881

@jfy133

* 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 <anoronh4@users.noreply.github.com> Co-authored-by: Juan Blanco Heredia <135283452+jblancoheredia@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <mirp.julia@gmail.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se> Co-authored-by: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> * 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 <pininforthefjords@gmail.com> * refact: use formula in `variancepartition/dream` only * docs: remove meta example --------- Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> --------- Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> * 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 <91951607+sofstam@users.noreply.github.com> * 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 <jin.khoo@campus.lmu.de> * 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 <38420248+Bisho2122@users.noreply.github.com> * 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 <33637490+sateeshperi@users.noreply.github.com> * 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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update nftest indentation * Update yml * Update tests and error handle --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Make database supply to GTDBTK classify WF more robust * Fix metadata * Update modules/nf-core/gtdbtk/classifywf/meta.yml Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Add plink2/maf module * Add plink2 HWE module * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/plink2/hwe/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * post review edit plink2 HWE module * edit plink2 HWE --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * renew snapshot * remove stub snapshots * remove config --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/svtk/rdtest2vcf/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * add tags * skip conda --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <louislenezet@gmaio.com> * Migrate `gem2/gem2bedmappability` to nf-test (#8275) Migrate to nf-test Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Migrate `gem2/gemmappability` to nf-test (#8278) Migrate to nf-test Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Migrate `genescopefk` to nf-test (#8277) * Migrate to nf-test * Add parameters * Update modules/nf-core/genescopefk/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/genescopefk/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <louislenezet@gmaio.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> * Fix whitespace --------- Co-authored-by: Daniel Schmitz <daniel.schmitz@gu.se> Co-authored-by: Sara Monzón <sara.monzon.fdz@gmail.com> Co-authored-by: Anne Marie Noronha <9613506+anoronh4@users.noreply.github.com> Co-authored-by: Anne Marie Noronha <anoronh4@users.noreply.github.com> Co-authored-by: Juan Blanco Heredia <135283452+jblancoheredia@users.noreply.github.com> Co-authored-by: Erik Fasterius <erik.fasterius@outlook.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se> Co-authored-by: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: nguyent-son <sonnguyen.msbio@gmail.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Kübra Narcı <kbrnrc@gmail.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Abhilesh Dhawanjewar <2447878+abhilesh@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Ding Yang Wang <82537687+Dewey-Wang@users.noreply.github.com> Co-authored-by: Bishoy Wadie <38420248+Bisho2122@users.noreply.github.com> Co-authored-by: ignatiusm <11403879+ignatiusm@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: jodennehy <jd41@sanger.ac.uk> Co-authored-by: Niklas Schandry <niklas@bio.lmu.de> Co-authored-by: Matias Perrone <64040416+mantisps@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime Laurent <69277125+max-laurent@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Niklas Schandry <schandry@gmail.com>

* Module for PCA * Module for PCA * Module for PCA * Module for PCA * Module for PCA * testing conda * plinkpca * Fixed ivar modules (nf-core#7868) * fixed ivar variants module * updated snapshot ivar variants because versions change * fixed ivar consensus module * simplified snapshot for consensus test, same as ivar variants module * simplified snapshot for trim test, same as ivar variants module * updated snapshot for ivar trim and consensus modules * removed empty log file in ivar trim in snapshot * updated ivar version to last one * updated version also in conda env * updated version also in conda env in ivar consensus and variants * updated container version for ivar consensus and variants * updated snapshots again * Update FastK + MerquryFK versions + allow conda, add merquryfk/hapmaker module, port to nf-test (nf-core#7847) * Start updating FastK modules to allow conda * Migrate all Merquryfk modules to nf-test * Update to container with explicit R * Fix container for FastK * Start fixing fastk modules * Fix FastK tests, add merquryfk/hapmaker module * Fix linting for some merquryFK modules * Fix merquryfk/merquryfk linting * Fix linting for everything except hapmaker * Fix snapshots? * Update tests * Fix tests pt 1000 * Sort fastk/merge test inputs to try and ensure repeatability * Rename output channels to avoid linting error * Fix hapmaker snapshot * Harshill alignment * Stub output format determined by args; add details to meta.yml files to disambiguate meta maps * Remove def again from variables - causes error otherwise * Fix Fastk/merge stub * Update snapshot * Fix rnaseq preprocessing: don't trim with bad linting (nf-core#7881) * Update versions for motus/preplong (nf-core#7854) * Update versions for motus preplong * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> * Versions * Add tests for downloaddb * Add snapshot * Update to the latest motus merge * Update motus merge * Remove pytest * Update pytest * Update downloaddb * Update modules/nf-core/motus/downloaddb/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add stub * Add stub --------- Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fixed conda channel order for fq module (nf-core#7871) (nf-core#7873) * Fixed conda channel order for fq module (nf-core#7871) By listing bioconda as the primary channel, the fq package can be installed and used in conda environments. modified: modules/nf-core/fq/generate/environment.yml modified: modules/nf-core/fq/lint/environment.yml modified: modules/nf-core/fq/subsample/environment.yml * added channel order comment to avoid a regression --------- Co-authored-by: Angel Pizarro <pizarroa@amazon.com> * New module: `khmer/trimlowabund` (nf-core#7806) * add khmer/trimlowabund * use evironment.yml * chore(deps): update tj-actions/changed-files action to v46 (nf-core#7809) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added coreograph nf-test (nf-core#7812) coreograph nf-test * Added ilastik/multicut nftest (nf-core#7811) * main.nf changes * finished test * Update `graphtyper/vcfconcatenate`: Add batching to avoid long command line error (nf-core#7805) add batching to vcfconcatenate to avoid long command line error Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> * basicpy nf-test (nf-core#7772) * basicpy nf-test * removed leftover pytest * separate output files * updated meta * separated outputs * adapted test * adapted inputs and snapshot * removed pytest files --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Clair3 (nf-core#7765) * Adds Clair3 * Removes TODOs and changes container urls * Changes bash command * Removes useless code lines * Removes TODO statements * Update meta.yml adds more file info to meta.yml * Update main.nf.test removes TODO and updates clair3 model directory * Update meta.yml fixes doi link * Add suggestions and changes data pulling * Fix main.nf.test adds correct structure to pass data to main * fix yaml * fix yaml final one * Update test snapshot * Fix snapshot * Fix tests * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/clair3/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Change meta description * Update meta * Update meta * update screenshot * Update modules/nf-core/clair3/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * chore(deps): update github actions (nf-core#7796) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Change file name for severus_somatic.vcf (nf-core#7814) * Change file name for severus_somatic.vcf * Update snapshot * Update yaml * Clean up hifiasm module + add bin file input (nf-core#7802) * Tidy hifiasm model + update tests * Update nf.test * Fix linting * Add fasta and PAF outputs to hifiasm; combine all bin files into a single output channel. Update documentation * Improve descriptiveness of output channel names * fix samtools/convert stub (nf-core#7816) * add default memory if task.memory is not set * Update modules/nf-core/khmer/trimlowabund/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/khmer/trimlowabund/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update `sourmash/compare`: Name output by prefix and update conda/docker (nf-core#7808) * update sourmash/compare so output is named by prefix * add stub to sourmash/sketch * Update modules/nf-core/sourmash/sketch/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * move test for sourmash/gather from pytest to nf-test * migrated sourmash taxannotate to nf-test --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * add Subworkflow linting step to CI (nf-core#7835) add swf linting step * Add missing swf change detection (nf-core#7836) * add swf linting step * add missing change detection for subworkflows * Add bedtools/shuffle module (nf-core#7803) * Add bedtools/shuffle module * Make linter happy * Update test snapshots for bedtools/shuffle * add new ARCHIVE_EXTRACT subworkflow (nf-core#7817) * add new subworkflow * rename * fix tags * add basic meta.yml * better comments * Update subworkflows/nf-core/archive_extract/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * APPLYBQSR output line specificity (nf-core#7818) * updated output line and snap file * linting fix in meta * Trying out RunsOn runners (nf-core#7840) * Trying out RunsOn runners * try older image * add debugging * fix action * pin setup-apptainer * add gpu test * fix usage syntax * switch from docker_self_hosted to docker * remove test comments * Fix language server error in salmon/quant (nf-core#7843) * New module: `busco/download` (nf-core#7788) * add busco/download * add author/maintainer * update tests snap for new conda version * revert to older conda version to match container versions * update tests * add stub * removed unneeded code in stub --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> * Fix language server errors in arriba/arriba (nf-core#7845) * name output by prefix * set to process_medium * check if input and output file are the same * make sure regex matches only part of string * Update modules/nf-core/khmer/trimlowabund/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/khmer/trimlowabund/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * apply changes made to file path handeling to stub * Update modules/nf-core/khmer/trimlowabund/meta.yml * Update modules/nf-core/khmer/trimlowabund/meta.yml --------- Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: John Orgera <65687576+johnoooh@users.noreply.github.com> * Added cram output to samtools/fixmate (nf-core#7820) * Added cram output to samtools/fixmate * Fixed tag * Fixed tag * Fixed linting * Updated onts * Use nft-bam, update output glob * Fixed meta.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Migrate `ATAQV/MKARV` to nf-test (nf-core#7893) Migrate to nf-test Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Added repeatmasker/repeatmasker (nf-core#7825) * Added repeatmasker/repeatmasker * Added onts * Added mdust (nf-core#7823) * Added mdust * Responded to review * Added agat/spfilterbyorfsize (nf-core#7822) * Added agat/spfilterbyorfsize * Added Gff tests * Migrate `authentict/deam2cont` to nf-test (nf-core#7947) * Update to nf-test * Fix samtools version * Update modules/nf-core/authentict/deam2cont/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/authentict/deam2cont/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/authentict/deam2cont/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Migrate `BAMTOOLS/CONVERT` to nf-test (nf-core#7958) * Migrate to nf-test * Update modules/nf-core/bamtools/convert/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/bamtools/convert/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update variable names * Fix spacing --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated deevariant to avoid failing nf-test (nf-core#7960) Updated the main to avoid failing nf-test * answer review Edo * fixing logfile * fixing variable name bug * rebasing * fixing variable name bug * fixing variable name bug --------- Co-authored-by: Bruno Ariano <bruno.ariano@fht.org> Co-authored-by: Sara Monzón <sara.monzon.fdz@gmail.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Angel Pizarro <delagoya@gmail.com> Co-authored-by: Angel Pizarro <pizarroa@amazon.com> Co-authored-by: Zachary Foster <zacharyfoster1989@gmail.com> Co-authored-by: Zachary Foster <fosterz@pop-os.localdomain> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: John Orgera <65687576+johnoooh@users.noreply.github.com> Co-authored-by: Usman Rashid <usman@smme.edu.pk> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Solenne Correard <54953390+scorreard@users.noreply.github.com>

Fix to nf-core#7881

@jfy133

* 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 <anoronh4@users.noreply.github.com> Co-authored-by: Juan Blanco Heredia <135283452+jblancoheredia@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <mirp.julia@gmail.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se> Co-authored-by: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> * 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 <pininforthefjords@gmail.com> * refact: use formula in `variancepartition/dream` only * docs: remove meta example --------- Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> --------- Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> * 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 <91951607+sofstam@users.noreply.github.com> * 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 <jin.khoo@campus.lmu.de> * 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 <38420248+Bisho2122@users.noreply.github.com> * 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 <33637490+sateeshperi@users.noreply.github.com> * 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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/clair3/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update nftest indentation * Update yml * Update tests and error handle --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Make database supply to GTDBTK classify WF more robust * Fix metadata * Update modules/nf-core/gtdbtk/classifywf/meta.yml Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Add plink2/maf module * Add plink2 HWE module * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/plink2/hwe/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/plink2/hwe/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * post review edit plink2 HWE module * edit plink2 HWE --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/survivor/filter/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * renew snapshot * remove stub snapshots * remove config --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/svtk/rdtest2vcf/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * add tags * skip conda --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <louislenezet@gmaio.com> * Migrate `gem2/gem2bedmappability` to nf-test (nf-core#8275) Migrate to nf-test Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Migrate `gem2/gemmappability` to nf-test (nf-core#8278) Migrate to nf-test Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * 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 <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/genescopefk/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <louislenezet@gmaio.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> * Fix whitespace --------- Co-authored-by: Daniel Schmitz <daniel.schmitz@gu.se> Co-authored-by: Sara Monzón <sara.monzon.fdz@gmail.com> Co-authored-by: Anne Marie Noronha <9613506+anoronh4@users.noreply.github.com> Co-authored-by: Anne Marie Noronha <anoronh4@users.noreply.github.com> Co-authored-by: Juan Blanco Heredia <135283452+jblancoheredia@users.noreply.github.com> Co-authored-by: Erik Fasterius <erik.fasterius@outlook.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se> Co-authored-by: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: nguyent-son <sonnguyen.msbio@gmail.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Kübra Narcı <kbrnrc@gmail.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Abhilesh Dhawanjewar <2447878+abhilesh@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Ding Yang Wang <82537687+Dewey-Wang@users.noreply.github.com> Co-authored-by: Bishoy Wadie <38420248+Bisho2122@users.noreply.github.com> Co-authored-by: ignatiusm <11403879+ignatiusm@users.noreply.github.com> Co-authored-by: robert-a-forsyth <robert.alexander.forsyth@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: jodennehy <jd41@sanger.ac.uk> Co-authored-by: Niklas Schandry <niklas@bio.lmu.de> Co-authored-by: Matias Perrone <64040416+mantisps@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime Laurent <69277125+max-laurent@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Niklas Schandry <schandry@gmail.com>

Fix rnaseq preprocessing: don't trim with bad linting

f1b81e3

pinin4fjords mentioned this pull request Mar 21, 2025

make trimming input reliant on fq lint output nf-core/rnaseq#1514

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itrujnara approved these changes Mar 21, 2025

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Merged via the queue into master with commit 8269755 Mar 21, 2025

pinin4fjords deleted the rnaseq_prepro_notrim_badlint branch March 21, 2025 15:09

bruno-ariano pushed a commit to HTGenomeAnalysisUnit/nf-core-modules that referenced this pull request Mar 24, 2025

Fix rnaseq preprocessing: don't trim with bad linting (nf-core#7881)

e9353a3

zachary-foster pushed a commit to zachary-foster/modules that referenced this pull request Mar 27, 2025

Fix rnaseq preprocessing: don't trim with bad linting (nf-core#7881)

be66da9

pinin4fjords added a commit that referenced this pull request Apr 7, 2025

Fix to #7881

e7b9035

pinin4fjords mentioned this pull request Apr 7, 2025

Fix to rnaseq preprocessing linting fix #8221

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github-merge-queue Bot pushed a commit that referenced this pull request Apr 7, 2025

Fix to rnaseq preprocessing linting fix (#8221)

a9d1fd8

Fix to #7881

pinin4fjords mentioned this pull request Apr 7, 2025

Update preprocessing subworkflow to fix linting block on trimming nf-core/rnaseq#1523

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SPPearce pushed a commit that referenced this pull request Apr 14, 2025

Fix to rnaseq preprocessing linting fix (#8221)

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Fix to #7881

famosab pushed a commit to famosab/modules that referenced this pull request Jun 3, 2025

Fix rnaseq preprocessing: don't trim with bad linting (nf-core#7881)

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famosab pushed a commit to famosab/modules that referenced this pull request Jun 3, 2025

Fix to rnaseq preprocessing linting fix (nf-core#8221)

64e8319

Fix to nf-core#7881

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Fix rnaseq preprocessing: don't trim with bad linting - #7881

Fix rnaseq preprocessing: don't trim with bad linting#7881
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