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

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

Align reads to a reference genome using bowtie

align map fastq fasta genome reference

Latest version: 0.0.0-6c4ed3a

Total downloads: 12

Source: nf-core/modules

Authors: @kevinmenden

Maintainers: @kevinmenden

Align reads to a reference genome using bowtie

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

include { BOWTIE_ALIGN } from 'nf-core/bowtie/align'

MIT License

Process

`Name`	`BOWTIE_ALIGN`

Input 3 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 genome information e.g. [ id:'sarscov2' ]
`index` file	Bowtie genome index files `*.ebwt`

`save_unaligned` boolean	Whether to save fastq files containing the reads which did not align.

Output 6 channels

#1 bam tuple

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

#2 log tuple

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

#3 fastq tuple

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

#4 versions_gzip tuple

`${task.process}` string	The name of the process
`gzip` string	The name of the tool
`gzip --version 2>&1 \| sed '1!d;s/gzip //'` eval	The expression to obtain the version of the tool

#5 versions_bowtie tuple

`${task.process}` string	The name of the process
`bowtie` string	The name of the tool
`bowtie --version 2>&1 \| sed -n 's/.*bowtie-align-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
bowtie	bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome.	http://bowtie-bio.sourceforge.net/index.shtml

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:07:46 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbowtie%2Falign/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bowtie/align/blobs/sha256:a3c2558260627700f023cd121926e89ed5a8041582f4fe11180be48ec6672447
Size	3.6 KB