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

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

Produces a consensus FASTA/FASTQ/PILEUP

consensus bam fastq fasta pileup

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @LilyAnderssonLee

Maintainers: @LilyAnderssonLee @matthdsm

Produces a consensus FASTA/FASTQ/PILEUP

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

include { SAMTOOLS_CONSENSUS } from 'nf-core/samtools/consensus'

MIT License

Process

`Name`	`SAMTOOLS_CONSENSUS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`input` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`index` file	BAM/CRAM index file `*.{bai,crai}`

Output 4 channels

#1 fasta tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.fasta` file	Consensus FASTA file `*.{fasta}`

#2 fastq tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.fastq` file	Consensus FASTQ file `*.{fastq}`

#3 pileup tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.pileup` file	Consensus PILEUP file `*.{pileup}`

#4 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
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 19:33:30 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fconsensus/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/consensus/blobs/sha256:40235a0f018b9da1392a73f0fc993ca3a0cba7eb4e57155dba32b94d30b15eb8
Size	2.8 KB
Checksum	sha256:40235a0f018b9da1392a73f0fc993ca3a0cba7eb4e57155dba32b94d30b15eb8
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:42:12 (UTC)		5	2.8 KB
0.0.0-0c7146d	08 Apr 2026 19:33:30 (UTC)		3	2.8 KB