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nf-core/somalier/extract @ 0.0.0-6c4ed3a

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

relatedness QC bam cram vcf gvcf ancestry identity kinship informative sites family
Latest version: 0.0.0-6c4ed3a
Total downloads: 9
Source: nf-core/modules
Authors: @ashotmarg @nvnieuwk
Maintainers: @ashotmarg @nvnieuwk

Summary

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

Get started

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

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

License

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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:46:51 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fsomalier%2Fextract/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/somalier/extract/blobs/sha256:b11781fa3c5a2307f2319b3fd57ce6e434108e16af8e539ab39d58e398271822
Size 2.7 KB
Checksum sha256:b11781fa3c5a2307f2319b3fd57ce6e434108e16af8e539ab39d58e398271822
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:46:51 (UTC) 3 2.7 KB
0.0.0-3fc6d40 22 Apr 2026 15:32:21 (UTC) 3 2.7 KB