modules/bwa_mem

Performs fastq alignment to a fasta reference using BWA

membwaalignmentmapfastqbamsam

https://github.com/nf-core/modules/[...]/modules/nf-core/bwa/mem

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}

`fasta` (file)

Reference genome in FASTA format

*.{fasta,fa}

`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}

`cram` (file)

Output CRAM file containing read alignments

*.{cram}

`csi` (file)

Optional index file for BAM file

*.{csi}

`crai` (file)

Optional index file for CRAM file

*.{crai}

`versions` (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.

http://bio-bwa.sourceforge.net bio-bwa.sourceforge.net/bwa.

modules/bwa_mem

Description