Nextflow Registry | nf-core/bismark/coverage2cytosine@0.0.0-6c4ed3a

nf-core/bismark/coverage2cytosine @ 0.0.0-6c4ed3a

Relates methylation calls back to genomic cytosine contexts.

Latest version: 0.0.0-6c4ed3a

Total downloads: 13

Source: nf-core/modules

Authors: @ewels

Maintainers: @ewels @sateeshperi

Relates methylation calls back to genomic cytosine contexts.

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

include { BISMARK_COVERAGE2CYTOSINE } from 'nf-core/bismark/coverage2cytosine'

MIT License

Process

`Name`	`BISMARK_COVERAGE2CYTOSINE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`coverage_file` file	A file containing methylation calls per position, in the format produced by bismark_methylation_extractor.

#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 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*report.txt.gz` file	Genomic cytosine context results. `*report.txt.gz`

#2 summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*cytosine_context_summary.txt` file	Cyotosine context summary report. `*cytosine_context_summary.txt`

#3 coverage tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cov.gz` file	A file containing methylation calls per position. `*.cov.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 15:06:30 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbismark%2Fcoverage2cytosine/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bismark/coverage2cytosine/blobs/sha256:1f1068e967e006b6b286d1657e26c01ec032f7f4cfa3e7768f5e82145bef27e0
Size	3.0 KB
Checksum	sha256:1f1068e967e006b6b286d1657e26c01ec032f7f4cfa3e7768f5e82145bef27e0
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:06:30 (UTC)		3	3.0 KB