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nf-core
Repository to host tool-specific module files for the Nextflow DSL2 community!
## WARNING - [ ] I have made sure to update the singularity and conda images This PR contains the following updates: | Package | Type | Update | Change...
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## PR checklist Closes #5621 - [ ] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be...
Closes #2700. with this PR, by defining the input channel `save_trimmed_pass` a user can define whether trimmed fastqs are written/saved, or not. This works for all three modes: interleaved, single_end,...
## PR checklist Closes #5627 Primary unfiltered alignment bam file and index now returned by the `fastq_align_bamcmp_bwa` subworkflow so that unmapped reads to the primary alignment can accessed. - [x]...
## PR checklist **Purpose:** This PR adds a subworkflow that combines multiple mmseqs tools. **Function:** This adds taxonomic classification to input 'nucleotide' sequences (e.g. contigs) , which can potentially be...
## PR checklist Closes #5621 - [ ] 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 Following on from issue #5564 which was addressed by #5565 where the alignment stats of the primary alignment are...
Module to extract ribosomal RNA from gtf file ## PR checklist - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or...
- Unzip the input file if it has .gz extension - Use the unzipped file for prediction - Provide output according to the prefix of the input tuple
Starting the process of updating fgbio versions. This is porting the modules from [fastquorum](https://github.com/nf-core/fastquorum), updating them to the most recent fgbio version and swapping to nf-test
