nf-core_modules/modules/bwa/mem/meta.yml
Maxime U. Garcia 1765225042
Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125)
* feat: view is now in args2 so we can use sort

* forgot one split_cpus

* feat: update with new logic

* fix: add more info

* fix: remove split_cpus logic
2021-12-08 14:31:27 +00:00

50 lines
1.4 KiB
YAML

name: bwa_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
- mem
- bwa
- alignment
- map
- fastq
- bam
- sam
tools:
- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@jeremy1805"