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}

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (file)

Reference genome in FASTA format

*.{fa,fasta,fna}

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

]

sam (file)

Output SAM file containing read alignments

*.{sam}

bam (file)

Output BAM file containing read alignments

*.{bam}

cram (file)

Output CRAM file containing read alignments

*.{cram}

crai (file)

Index file for CRAM file

*.{crai}

csi (file)

Index file for BAM file

*.{csi}

versions (file)

File containing software versions

versions.yml
included in
callingcards hgtseq nascent radseq raredisease rnadnavar sarek
maintainers
Github user maxulysse
Github user matthdsm
get in touch
Ask a question on Slack Open an issue on GitHub

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