gatk4-applyvqsr #2
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* isoseq3/cluster: migrate to nf-test * isoseq3/cluster Fix typos * isoseq3/refine update to version 4.0.0 and migrate to nf-test * isoseq3/refine Fix linting * isoseq3 /refine Update script path * pbccs migrate to nf-test * pbbam/pbmerge migrate to nf-test * lima update to 2.9.0 and migrate to nf-test * Remove modules from pytest_modules.yml isoseq/cluster, isoseq/refine, lima, pbccs, pbbam/pbmerge * Rename isoseq3 to isoseq * Update isoseq/cluster and isoseq/refine snap * Update pbbam/pbmerge snap * Revert pbbam/pbmerge snap Generated with singularity/docker profile * Update test dataset paths * Update test names * Add stub * Add stub tests * Apply Maxime's patch * Fix tests * Remove PublishDir in config * update snapshot * Fix test * Update test * Fix pbccs * Clean pbmerge config * Fix isoseq/refine * Add version test to isoseq refine * Fix pbmerge versions test * removed pbbam module PacBio have change their program organisation. Pbmerge is now included into pbtk. * Rollback pbmerge to original state * remove accidentally added vscode config * Update tests/config/pytest_modules.yml Co-authored-by: Famke Bäuerle <[email protected]> * fix pytest_modules.yml * prettier --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Simon Pearce <[email protected]>
* Add Bracken stub, nf-test, version bump * Remove debug TODOs and fix tags * Remove pytests * And the other file * Add nf-test, stub, and version bump bracken combine versions * Fix tags * Add BRACKEN/BUILD module * Apply suggestions from code review Co-authored-by: Carson J Miller <[email protected]> * Add additional output channel for secutiry * Make internal `mv` commands less error rone * Align semi colons --------- Co-authored-by: Carson J Miller <[email protected]>
famosab
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Jun 25, 2024
* Added metaphlan subworkflow * Removed extra index line * Added config * Updated meta.yml, removed comments * Apply suggestions from code review Co-authored-by: Carson J Miller <[email protected]> * Updated test snapshot * Updated test snapshot #2 * Apply suggestions from code review * Sort output by file name * Changed sort; modified test dataset used * Changed sort method to file name --------- Co-authored-by: Carson J Miller <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Carson J Miller <[email protected]>
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