New module: khmer/trimlowabund#7806
Merged
zachary-foster merged 36 commits intonf-core:masterfrom Mar 21, 2025
Merged
Conversation
added 2 commits
March 14, 2025 15:13
zachary-foster
changed the title
khmer/trimlowabund
SPPearce
reviewed
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
reviewed
Mar 18, 2025
Contributor
SPPearce
left a comment
SPPearce
left a comment
There was a problem hiding this comment.
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>
Contributor
Author
|
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
reviewed
Mar 20, 2025
Contributor
SPPearce
left a comment
SPPearce
left a comment
There was a problem hiding this comment.
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>
Contributor
Author
|
Ok, I made those changes. Good idea having the |
SPPearce
approved these changes
Mar 21, 2025
Contributor
SPPearce
left a comment
SPPearce
left a comment
There was a problem hiding this comment.
Ok, think that is good.
I've added some ontologies (if you can add these to modules going forward that'd be great)
bruno-ariano
pushed a commit
to HTGenomeAnalysisUnit/nf-core-modules
that referenced
this pull request
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>
github-merge-queue Bot
pushed a commit
that referenced
this pull request
Mar 26, 2025
* 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
added a commit
to zachary-foster/modules
that referenced
this pull request
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>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
10 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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.