Nextflow Registry | nf-core/biscuit/epiread@0.0.0-6c4ed3a

nf-core/biscuit/epiread @ 0.0.0-6c4ed3a

Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @njspix

Maintainers: @njspix @sateeshperi

Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.

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

include { BISCUIT_EPIREAD } from 'nf-core/biscuit/epiread'

MIT License

Process

`Name`	`BISCUIT_EPIREAD`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM file contained mapped reads

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bai` file	BAM file index

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`snp_bed` file	BED file containing SNP information (optional)

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Input genome fasta file

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`index` directory	Directory containing biscuit genome index

Output 3 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bed.gz` file	Gzipped BED file with methylation (and optionally SNV) information `*.{epiread.bed.gz}`

#2 versions_biscuit tuple

`${task.process}` string	The name of the process
`biscuit` string	The name of the tool
`biscuit version \|& sed '1!d; s/^.*BISCUIT Version: //'` eval	The expression to obtain the version of the tool

#3 versions_samtools tuple

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

Tool	Description	Homepage
biscuit	A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data	https://huishenlab.github.io/biscuit/

Downloads
Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:06:21 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbiscuit%2Fepiread/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/biscuit/epiread/blobs/sha256:2de81d1a5d1fa809f050a2facf06b1b1d1f6ad1634b0708d0639c2229e882294
Size	3.3 KB
Checksum	sha256:2de81d1a5d1fa809f050a2facf06b1b1d1f6ad1634b0708d0639c2229e882294