Nextflow Registry | nf-core/biscuit/pileup@0.0.0-0c7146d

nf-core/biscuit/pileup @ 0.0.0-0c7146d

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

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:27:14 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbiscuit%2Fpileup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/biscuit/pileup/blobs/sha256:4db8a0247ede88b5d0303b080c5f9cf112171e8d45c8ed0f7670ea8a6b65e663
Size	3.3 KB
Checksum	sha256:4db8a0247ede88b5d0303b080c5f9cf112171e8d45c8ed0f7670ea8a6b65e663
Downloads	1