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

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

Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.

fasta genome coverage

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @edmundmiller

Maintainers: @edmundmiller

Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.

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

include { BBMAP_PILEUP } from 'nf-core/bbmap/pileup'

MIT License

Process

`Name`	`BBMAP_PILEUP`

Input 1 channel

#1 tuple

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

Output 5 channels

#1 hist tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.hist.txt` file	Histogram of # occurrences of each depth level `*.hist.txt`

#2 covstats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.stats.txt` file	Coverage statistics `*.stats.txt`

#3 versions_pigz tuple

`${task.process}` string	The name of the process
`pigz` string	The name of the tool
`pigz --version 2>&1 \| sed "s/^.pigz[[:space:]]//"` eval	The expression to obtain the version of the tool

#4 versions_bbmap tuple

`${task.process}` string	The name of the process
`bbmap` string	The name of the tool
`bbversion.sh \| grep -v 'Duplicate cpuset'` eval	The expression to obtain the version of the tool

#5 versions_samtools tuple

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

Tool	Description	Homepage
bbmap	BBMap is a short read aligner, as well as various other bioinformatic tools.	https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:24:51 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Fpileup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bbmap/pileup/blobs/sha256:aba37118fd60e700e0a88f644fb06d556b62e7ad3457d01e03404c58a315e84b
Size	2.5 KB
Checksum	sha256:aba37118fd60e700e0a88f644fb06d556b62e7ad3457d01e03404c58a315e84b
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:24:51 (UTC)		1	2.5 KB	-