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: 0.0.0-6c4ed3a

Total downloads: 7

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	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 18:45:35 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Fpileup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bbmap/pileup/blobs/sha256:821beafc375e48c5f0522d73e4f595ceddb8e2944d2ad82c0f10e954f6253bdf
Size	2.5 KB
Checksum	sha256:821beafc375e48c5f0522d73e4f595ceddb8e2944d2ad82c0f10e954f6253bdf
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:04:43 (UTC)		4	2.5 KB
0.0.0-0c7146d	08 Apr 2026 18:45:35 (UTC)		3	2.5 KB