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

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

Performs fastq alignment to a fasta reference using BWA-MEME

mem bwa bwamem2 bwameme alignment map fastq bam sam cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

Performs fastq alignment to a fasta reference using BWA-MEME

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

include { BWAMEME_MEM } from 'nf-core/bwameme/mem'

MIT License

Process

`Name`	`BWAMEME_MEM`

Input 6 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`

`mbuffer` integer	memory for mbuffer in megabytes (default 3072)

`samtools_threads` integer	number of threads for samtools (default 2)

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_bwameme tuple

`${task.process}` string	The name of the process
`bwameme` string	The name of the tool
`1.0.6` string	The expression to obtain the version of the tool

#7 versions_samtools tuple

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

Tool