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

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

Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @njspix

Maintainers: @njspix @sateeshperi

Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants

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

include { BISCUIT_PILEUP } from 'nf-core/biscuit/pileup'

MIT License

Process

`Name`	`BISCUIT_PILEUP`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`normal_bams` file	BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a tumor BAM file is provided, exactly one normal (germline) BAM must be provided. `*.{bam}`
`normal_bais` file	BAM index file or files corresponding to the provided normal_bams `*.{bai}`
`tumor_bam` file	Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a tumor BAM file is provided, exactly one normal BAM must be provided. `*.{bam}`
`tumor_bai` file	Optional. BAM index file corresponding to provided tumor_bam `*.{bai}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Input genome fasta file

#3 tuple

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

Output 3 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	vcf file with methylation information `*.{vcf.gz}`

#2 versions_bgzip tuple

`${task.process}` string	The name of the process
`bgzip` string	The name of the tool
`bgzip --version \| head -1 \| sed "s/bgzip (htslib) //"` eval	The expression to obtain the version of the tool

#3 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

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

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:06:25 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbiscuit%2Fpileup/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/biscuit/pileup/blobs/sha256:873e0bd99bcd4060945e5bf6af6e7f30b1d832152b5a87f2ef7ad1ca3637412b
Size	3.3 KB
Checksum	sha256:873e0bd99bcd4060945e5bf6af6e7f30b1d832152b5a87f2ef7ad1ca3637412b
Downloads	4