Nextflow Registry | nf-core/bismark/align@0.0.0-0c7146d

nf-core/bismark/align @ 0.0.0-0c7146d

Performs alignment of BS-Seq reads using bismark

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @phue

Maintainers: @phue @sateeshperi

Performs alignment of BS-Seq reads using bismark

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

include { BISMARK_ALIGN } from 'nf-core/bismark/align'

MIT License

Process

`Name`	`BISMARK_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 sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Reference genome FASTA file

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`index` directory	Bismark genome index directory `BismarkIndex`

Output 4 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 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*report.txt` file	Bismark alignment reports `*{report.txt}`

#3 unmapped tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*fq.gz` file	Output FastQ file(s) containing unmapped reads `*.{fq.gz}`

#4 versions_bismark tuple

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

Tool	Description	Homepage
bismark	Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.	https://github.com/FelixKrueger/Bismark

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:27:20 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbismark%2Falign/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bismark/align/blobs/sha256:07519ec50f2b3aecbb80d966927d17f21189d9875dc38e615f0529b95cdcecd1
Size	3.6 KB
Checksum	sha256:07519ec50f2b3aecbb80d966927d17f21189d9875dc38e615f0529b95cdcecd1
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:27:20 (UTC)		1	3.6 KB	-