mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
43 lines
1.2 KiB
YAML
43 lines
1.2 KiB
YAML
|
name: bwa mem
|
||
|
|
description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner
|
||
|
|
keywords:
|
||
|
|
- mem
|
||
|
|
- bwa
|
||
|
|
- alignment
|
||
|
|
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
|
||
|
|
input:
|
||
|
|
-
|
||
|
|
- id:
|
||
|
|
type: val
|
||
|
|
description: read/read pair id
|
||
|
|
- reads:
|
||
|
|
type: file
|
||
|
|
description: Input fastq file
|
||
|
|
pattern: "*.{fastq,fq}"
|
||
|
|
- index:
|
||
|
|
type: file
|
||
|
|
description: bwa indexes file
|
||
|
|
pattern: "*.{amb,ann,bwt,pac,sa}"
|
||
|
|
- prefix:
|
||
|
|
type: val
|
||
|
|
description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
|
||
|
|
output:
|
||
|
|
-
|
||
|
|
- bam:
|
||
|
|
type: file
|
||
|
|
description: Output bam file
|
||
|
|
pattern: "*.bam"
|
||
|
|
- bamindex:
|
||
|
|
type: file
|
||
|
|
description: Output bam index file
|
||
|
|
pattern: "*.bai"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@jeremy1805"
|