Nextflow Registry | nf-core/bismark/methylationextractor@0.0.0-6c4ed3a

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

Extracts methylation information for individual cytosines from alignments.

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @phue

Maintainers: @phue @sateeshperi

Extracts methylation information for individual cytosines from alignments.

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

include { BISMARK_METHYLATIONEXTRACTOR } from 'nf-core/bismark/methylationextractor'

MIT License

Process

`Name`	`BISMARK_METHYLATIONEXTRACTOR`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM file containing read alignments `*.{bam}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`index` directory	Bismark genome index directory `BismarkIndex`

Output 6 channels

#1 mbias tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.M-bias.txt` file	Text file containing methylation bias information `*.{M-bias.txt}`

#2 report tuple

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

#3 bedgraph tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bedGraph.gz` file	Bismark output file containing coverage and methylation metrics `*.{bedGraph.gz}`

#4 coverage tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cov.gz` file	Bismark output file containing coverage metrics `*.{cov.gz}`

#5 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

#6 methylation_calls tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.txt.gz` file	Bismark output file containing strand-specific methylation calls `*.{txt.gz}`

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 15:07:26 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbismark%2Fmethylationextractor/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bismark/methylationextractor/blobs/sha256:1fa1057afa7336271c608bf140300ccc34eb09d71b8496ceaf0193460b58900f
Size	3.4 KB
Checksum	sha256:1fa1057afa7336271c608bf140300ccc34eb09d71b8496ceaf0193460b58900f