Nextflow Registry | nf-core/bwa/mem@0.0.0-6c4ed3a

nf-core/bwa/mem @ 0.0.0-6c4ed3a

Performs fastq alignment to a fasta reference using BWA

mem bwa alignment map fastq bam sam

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @drpatelh @jeremy1805 @matthdsm

Maintainers: @drpatelh @jeremy1805 @matthdsm

Performs fastq alignment to a fasta reference using BWA

Add the following snippet to your workflow script to include this module.

include { BWA_MEM } from 'nf-core/bwa/mem'

MIT License

Process

`Name`	`BWA_MEM`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`index` file	BWA genome index files `Directory containing BWA index *.{amb,ann,bwt,pac,sa}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Reference genome in FASTA format `*.{fasta,fa}`

`sort_bam` boolean	use samtools sort (true) or samtools view (false) `true or false`

Output 6 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information
`*.bam` file	Output BAM file containing read alignments `*.{bam}`

#2 csi tuple

`meta` map	Groovy Map containing sample information
`*.csi` file	Optional index file for BAM file `*.{csi}`

#3 crai tuple

`meta` map	Groovy Map containing sample information
`*.crai` file	Optional index file for CRAM file `*.{crai}`

#4 cram tuple

`meta` map	Groovy Map containing sample information
`*.cram` file	Output CRAM file containing read alignments `*.{cram}`

#5 versions_bwa tuple

`${task.process}` string	The name of the process
`bwa` string	The name of the tool
`bwa 2>&1 \| sed -n "s/^Version: //p"` eval	The expression to obtain the version of the tool

#6 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
bwa	BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.	http://bio-bwa.sourceforge.net/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:08:05 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbwa%2Fmem/0.0.0-6c4ed3a/download