Description

Performs fastq alignment to a fasta reference using BWA

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/index information
e.g. [ id:‘test’ ]

index (file)

BWA genome index files

Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}

sort_bam (boolean)

use samtools sort (true) or samtools view (false)

true or false

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Output BAM file containing read alignments

*.{bam}

versions (file)

File containing software versions

versions.yml
included in
callingcards hgtseq nascent radseq raredisease rnadnavar sarek
author
Github user maxulysse
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Tools

bwa
MIT

BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

github.com/bwa-mem2/bwa-mem2 http://www.htslib.org/doc/samtools