Nextflow Registry | nf-core/bwamem2/mem@0.0.0-6c4ed3a

nf-core/bwamem2/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: 6

Source: nf-core/modules

Authors: @maxulysse @matthdsm

Maintainers: @maxulysse @matthdsm

Performs fastq alignment to a fasta reference using BWA

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

include { BWAMEM2_MEM } from 'nf-core/bwamem2/mem'

MIT License

Process

`Name`	`BWAMEM2_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/index information e.g. [ id:'test' ]
`index` file	BWA genome index files `Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}`

#3 tuple

`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 7 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bam` file	Output BAM file containing read alignments `*.{bam}`

#2 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.csi` file	Index file for BAM file `*.{csi}`

#3 sam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sam` file	Output SAM file containing read alignments `*.{sam}`

#4 crai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.crai` file	Index file for CRAM file `*.{crai}`

#5 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cram` file	Output CRAM file containing read alignments `*.{cram}`

#6 versions_bwamem2 tuple

`${task.process}` string	The name of the process
`bwamem2` string	The name of the tool
`bwa-mem2 version \| grep -o -E "[0-9]+(\.[0-9]+)+"` eval	The expression to obtain the version of the tool

#7 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-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.	https://github.com/bwa-mem2/bwa-mem2

Version	0.0.0-6c4ed3a