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

Performs alignment of BS-Seq reads using bismark

bismark 3-letter genome map methylation 5mC methylseq bisulphite bisulfite bam
Latest version: 0.0.0-6c4ed3a
Total downloads: 14
Source: nf-core/modules
Authors: @phue
Maintainers: @phue @sateeshperi

Summary

Performs alignment of BS-Seq reads using bismark

Get started

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

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

License

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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:06:29 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fbismark%2Falign/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bismark/align/blobs/sha256:7ee234291e6f22aac6b599ae4789a3dfdab5ca4916b64d9f579bd409bf796d8f
Size 3.7 KB
Checksum sha256:7ee234291e6f22aac6b599ae4789a3dfdab5ca4916b64d9f579bd409bf796d8f
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:06:29 (UTC) 3 3.7 KB
0.0.0-7f68141 16 Apr 2026 15:00:13 (UTC) 4