Nextflow Registry | nf-core/bcftools/mpileup@0.0.0-6c4ed3a

nf-core/bcftools/mpileup @ 0.0.0-6c4ed3a

Compresses VCF files

variant calling mpileup VCF

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @joseespinosa

Maintainers: @joseespinosa

Compresses VCF files

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

include { BCFTOOLS_MPILEUP } from 'nf-core/bcftools/mpileup'

MIT License

Process

`Name`	`BCFTOOLS_MPILEUP`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Input BAM file `*.{bam}`
`intervals_mpileup` file	Input intervals file. A file (commonly '.bed') containing regions to subset used by mpileup
`intervals_call` file	Input intervals file. A file (commonly '.bed') containing regions to subset used by call but need a fourth column with REF,ALT

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	FASTA reference file `*.{fasta,fa}`
`fai` file	FASTA reference file index `*.fai`

`save_mpileup` boolean	Save mpileup file generated by bcftools mpileup

Output 5 channels

#1 tbi tuple

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

#2 vcf tuple

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

#3 stats tuple

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

#4 mpileup tuple

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

#5 versions_bcftools tuple

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

Tool	Description	Homepage
mpileup	Generates genotype likelihoods at each genomic position with coverage.	http://samtools.github.io/bcftools/bcftools.html

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:05:00 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fmpileup/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bcftools/mpileup/blobs/sha256:ee198101d07d50e8f06a8004c56849d14532dac499cebab471b32188d1488c49
Size	3.9 KB
Checksum	sha256:ee198101d07d50e8f06a8004c56849d14532dac499cebab471b32188d1488c49
Downloads	5