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 information.
e.g. [ id:‘test’, single_end

]

index (file)

BWA genome index files

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

sort_bam (boolean)

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

true or false

Output

Name (Type)
Description
Pattern

bam (file)

Output BAM file containing read alignments

*.{bam}

versions (file)

File containing software versions

versions.yml
included in
atacseq chipseq crisprseq hgtseq hicar nascent pathogensurveillance radseq rnadnavar sarek ssds variantcatalogue
authors
Github user drpatelh Github user jeremy1805
get in touch
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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 http://www.htslib.org/doc/samtools.html