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

]

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

]

index (file)

BWA genome index files

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

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

sai (file)

Single or paired SA coordinate files

*.sai
included in
callingcards sammyseq
maintainers
Github user jfy133
Github user gallvp
get in touch
Ask a question on Slack Open an issue on GitHub

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.

http://bio-bwa.sourceforge.net bio-bwa.sourceforge.net/bwa. 10.1093/bioinformatics/btp324