Description

Find SA coordinates of the input reads for bwa short-read mapping

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

reads:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

meta2:map

Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]

index:file

BWA genome index files

Directory containing BWA index *.{amb,ann,bwt,pac,sa}

Output

name:type
description
pattern

sai

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.sai:file

Single or paired SA coordinate files

*.sai

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bwa
GPL-3.0-or-later

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.