Nextflow Registry | nf-core/somalier/extract@0.0.0-0c7146d

nf-core/somalier/extract @ 0.0.0-0c7146d

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ashotmarg @nvnieuwk

Maintainers: @ashotmarg @nvnieuwk

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

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

include { SOMALIER_EXTRACT } from 'nf-core/somalier/extract'

MIT License

Process

`Name`	`SOMALIER_EXTRACT`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file
`input_index` file	index file of the input data, e.g., bam.bai, cram.crai

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'hg38' ]
`fasta` file	The reference fasta file `*.{fasta,fna,fas,fa}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'hg38' ]
`fai` file	FASTA index file `*.fai`

#4 tuple

`meta4` map	Groovy Map containing sites information e.g. [ id:'hg38' ]
`sites` file	sites file in VCF format which can be taken from https://github.com/brentp/somalier `*.vcf.gz`

Output 2 channels

#1 extract tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.somalier` file	binary output file based on extracted sites `*.{somalier}`

#2 versions_somalier tuple

`${task.process}` string	The name of the process
`somalier` string	The name of the tool
`somalier 2>&1 \| sed -n 's/.version: $[0-9.]$.*/\1/p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
somalier	Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs	https://github.com/brentp/somalier

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:15:38 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsomalier%2Fextract/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/somalier/extract/blobs/sha256:545f935ae09b08de89cc9cb38e8df6cc435a4b6c83315aedfa283a7818fdba99
Size	2.6 KB
Checksum	sha256:545f935ae09b08de89cc9cb38e8df6cc435a4b6c83315aedfa283a7818fdba99
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:15:38 (UTC)		1	2.6 KB	-