Nextflow Registry | nf-core/samtools/mpileup@0.0.0-0c7146d

nf-core/samtools/mpileup @ 0.0.0-0c7146d

Generate text pileup output for one or multiple BAM files. Each input file produces a separate group of pileup columns in the output.

mpileup bam sam cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @drpatelh @joseespinosa

Maintainers: @joseespinosa @krannich479 @matthdsm

Generate text pileup output for one or multiple BAM files. Each input file produces a separate group of pileup columns in the output.

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

include { SAMTOOLS_MPILEUP } from 'nf-core/samtools/mpileup'

MIT License

Process

`Name`	`SAMTOOLS_MPILEUP`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`input` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`index` file	CSI/BAI/CRAI file. Optional. Only required when using the '-r' parameter. `*.{bai,crai,csi}`
`intervals` file	Interval FILE. Optional. `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta` file	FASTA reference file. Optional. `*.{fasta,fa,fna}`
`fai` file	FAI file. Optional. Only required (recommended) when using the '-f' parameter. `*.{fai}`

Output 2 channels

#1 mpileup tuple

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

#2 versions_samtools tuple

`${task.process}` string	The process the versions were collected from
`samtools` string	The tool name
`samtools version \| sed '1!d;s/.* //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
samtools	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:34:02 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fmpileup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/mpileup/blobs/sha256:9f962eed20befe76003302f176427933bfab816d9dffb65cbc4f88f5729b8ddc
Size	3.0 KB
Checksum	sha256:9f962eed20befe76003302f176427933bfab816d9dffb65cbc4f88f5729b8ddc
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:43:20 (UTC)		5	3.0 KB
0.0.0-0c7146d	08 Apr 2026 19:34:02 (UTC)		3	3.0 KB