Nextflow Registry | nf-core/ngscheckmate/ncm@0.0.0-6c4ed3a

nf-core/ngscheckmate/ncm @ 0.0.0-6c4ed3a

Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.

ngscheckmate matching snp

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @sppearce

Maintainers: @sppearce

Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.

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

include { NGSCHECKMATE_NCM } from 'nf-core/ngscheckmate/ncm'

MIT License

Process

`Name`	`NGSCHECKMATE_NCM`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`files` file	VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too. `*.{vcf,vcf.gz,bam,bai}`

#2 tuple

`meta2` map	Groovy Map containing SNP information e.g. [ id:'test' ]
`snp_bed` file	BED file containing the SNPs to analyse `*.{bed}`

#3 tuple

`meta3` map	Groovy Map containing reference fasta index information e.g. [ id:'test' ]
`fasta` file	fasta file for the genome, only used in the bam mode `*.{fasta}`
`fai` file	fasta index file for the genome, only used in the bam mode `*.{fai}`

Output 6 channels

#1 all tuple

`meta` file	A text file containing the correlation matrix between each sample `*corr_matrix.txt`
`*_all.txt` file	A txt file containing all the sample comparisons, whether they match or not `*all.txt`

#2 pdf tuple

`meta` file	A text file containing the correlation matrix between each sample `*corr_matrix.txt`
`*.pdf` file	A pdf containing a dendrogram showing how the samples match up `*.{pdf}`

#3 vcf tuple

`meta` file	A text file containing the correlation matrix between each sample `*corr_matrix.txt`
`*.vcf` file	If ran in bam mode, vcf files for each sample giving the SNP calls used `*.vcf`

#4 matched tuple

`meta` file	A text file containing the correlation matrix between each sample `*corr_matrix.txt`
`*_matched.txt` file	A txt file containing only the samples that match with each other `*matched.txt`

#5 corr_matrix tuple

`meta` file	A text file containing the correlation matrix between each sample `*corr_matrix.txt`
`*_corr_matrix.txt` file	A text file containing the correlation matrix between each sample `*corr_matrix.txt`

#6 versions_ngscheckmate tuple

`${task.process}` string	The process the versions were collected from
`ngscheckmate` string	The tool name
`ncm.py --help \| sed '7!d;s/.* v//g'` string	The command used to generate the version of the tool

Tool	Description	Homepage
ngscheckmate	NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.	https://github.com/parklab/NGSCheckMate

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:33:11 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fngscheckmate%2Fncm/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextfl