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nf-core
Repository to host tool-specific module files for the Nextflow DSL2 community!
## PR checklist Closes #8691 - [ ] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be...
### Is your feature request related to a problem? Please describe Module `rundeepvariant` output channels include index-output, which currently supports `.tbi` format. Deepvariant also supports `.csi` index output, when the...
### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...
Issue: cellranger mkfastq outputs both fastq and fastq_idx files together which causes issues with some other processes (e.g. falco couldn't process index fastqs in the demultiplex pipeline). Solution: split the...
## PR checklist This PR aims to share across test the conda environment created. This create a `.nf-test/shared/conda` folder where the environment are stored. Therefore nf-test won't recreate it, if...
Add module taxonkit/list. Allows taxonids to be passed both as list on command and as file. Code structure is very similar to [taxonkit/lineage](https://github.com/nf-core/modules/tree/a923860fbba4d20a8aa8fac58311b8c232613690/modules/nf-core/taxonkit/lineage) - [x] This comment contains a description...
## PR checklist Closes #7878 Closes #8087 - [x] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that...
### Have you checked the docs? - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug In a freshly initialised nf-core project, running the commmand...
## PR checklist Closes #8031 - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...
## PR checklist Closes #XXX - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...