Nextflow Registry | nf-core/bowtie2/align@0.0.0-6c4ed3a

nf-core/bowtie2/align @ 0.0.0-6c4ed3a

Align reads to a reference genome using bowtie2

align map fasta fastq genome reference

Latest version: 0.0.0-6c4ed3a

Total downloads: 14

Source: nf-core/modules

Authors: @joseespinosa @drpatelh

Maintainers: @joseespinosa @drpatelh

Align reads to a reference genome using bowtie2

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

include { BOWTIE2_ALIGN } from 'nf-core/bowtie2/align'

MIT License

Process

`Name`	`BOWTIE2_ALIGN`

Input 5 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	Bowtie2 genome index files `*.ebwt`

#3 tuple

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

`save_unaligned` boolean	Save reads that do not map to the reference (true) or discard them (false) (default: false)

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

Output 10 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	Output SAM/BAM index for large inputs `*.csi`

#3 log tuple

`meta` map	Groovy Map containing sample information
`*.log` file	Alignment log `*.log`

#4 sam tuple

`meta` map	Groovy Map containing sample information
`*.sam` file	Output SAM file containing read alignments `*.sam`

#5 crai tuple

`meta` map	Groovy Map containing sample information
`*.crai` file	Output CRAM index `*.crai`

#6 cram tuple

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

#7 fastq tuple

`meta` map	Groovy Map containing sample information
`*fastq.gz` file	Unaligned FastQ files `*.fastq.gz`

#8 versions_pigz tuple

`pigz --version 2>&1 \| sed 's/pigz //'` eval
`${task.process}` string	The name of the process
`pigz` string	The name of the tool