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

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

A bioinformatics tool for working with modified bases

methylation ont long-read

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @Michal-Babins @fellen31

Maintainers: @fellen31 @jkh00

A bioinformatics tool for working with modified bases

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

include { MODKIT_PILEUP } from 'nf-core/modkit/pileup'

MIT License

Process

`Name`	`MODKIT_PILEUP`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`bam` file	Sorted BAM/CRAM file `*.{bam,cram}`
`bai` file	Associated index file for BAM `*.bai`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'hg38' ]`
`fasta` file	Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering `*.fasta`
`fai` file	Associated index file for FASTA `*.fai`

#3 tuple

`meta3` map	Groovy Map containing BED file information e.g. `[ id:'regions' ]`
`bed` file	BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the file `*.bed`

Output 3 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.log` file	File for debug logs to be written to `*.log`

#2 bedgz tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.bed.gz` file	bgzf-compressed bedMethyl output file(s) `*.bed`

#3 versions_modkit tuple

`${task.process}` string	The name of the process
`modkit` string	The name of the tool
`modkit --version \| sed 's/modkit //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
modkit	A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data	https://github.com/nanoporetech/modkit

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:56:56 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmodkit%2Fpileup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/modkit/pileup/blobs/sha256:71f33c1f9cc1d3b7bbeaaaf44af04a430ecee3e27d53797902b9fe11575d7271
Size	3.6 KB
Checksum	sha256:71f33c1f9cc1d3b7bbeaaaf44af04a430ecee3e27d53797902b9fe11575d7271
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:56:56 (UTC)		1	3.6 KB	-