New module: khmer/trimlowabund
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added 2 commits
March 14, 2025 15:13
zachary-foster
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khmer/trimlowabund
SPPearce
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Mar 17, 2025
coreograph nf-test
* main.nf changes * finished test
…d 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 * 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>
* 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>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* Change file name for severus_somatic.vcf * Update snapshot * Update yaml
* 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
SPPearce
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Mar 18, 2025
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Few questions.
What resources does the tool need? You've set process_low but then defaulting to 16G.
Is there a way to name the output file with prefix rather than the filename?
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
…ker (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 swf linting step
* add swf linting step * add missing change detection for subworkflows
* Add bedtools/shuffle module * Make linter happy * Update test snapshots for bedtools/shuffle
* 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>
* updated output line and snap file * linting fix in meta
* 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
* 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>
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Ok, I added code to make the name have the prefix in it while still preserving the original file extension and adding .gz if needed. |
SPPearce
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Mar 20, 2025
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Can you add the check that the output file isn't going to be the same as the input file, then I think it is good.
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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Ok, I made those changes. Good idea having the |
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Mar 21, 2025
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Ok, think that is good.
I've added some ontologies (if you can add these to modules going forward that'd be great)
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Mar 24, 2025
* 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>
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* 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>
zachary-foster
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Mar 27, 2025
* 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>
zachary-foster
added a commit
to zachary-foster/modules
that referenced
this pull request
Mar 27, 2025
* 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>
Dewey-Wang
pushed a commit
to Dewey-Wang/modules
that referenced
this pull request
Mar 28, 2025
* 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>
famosab
added a commit
to famosab/modules
that referenced
this pull request
Jun 3, 2025
* 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>
famosab
added a commit
to famosab/modules
that referenced
this pull request
Jun 3, 2025
* 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>
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Adds a new module for
trim-low-abund.pyfrom the khmer tool kit. This removes low abundance k-mers from reads, which is useful as a preprocessing step when making sketches of reads using tools likesourmash sketch.