Nextflow Registry | nf-core/ngscheckmate/vafncm@0.0.0-0c7146d

nf-core/ngscheckmate/vafncm @ 0.0.0-0c7146d

Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.

ngscheckmate matching snp qc

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @sppearce

Maintainers: @sppearce

Summary

Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.

Get started

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

include { NGSCHECKMATE_VAFNCM } from 'nf-core/ngscheckmate/vafncm'

License

MIT License

Process

`Name`	`NGSCHECKMATE_VAFNCM`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information about the combined set of files e.g. `[ id:'combined' ]`
`vafs` file	Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq `*.{vaf}`

Output 5 channels

#1 all tuple

`meta` map	Groovy Map containing sample information about the combined set of files e.g. `[ id:'combined' ]`
`*_all.txt` file	A txt file containing all the sample comparisons, whether they match or not `*all.txt`

#2 pdf tuple

`meta` map	Groovy Map containing sample information about the combined set of files e.g. `[ id:'combined' ]`
`*.pdf` file	A pdf containing a dendrogram showing how the samples match up.\| Note due to a bug in the R script used by the tool this is not produced when only two samples are given. `*.{pdf}`

#3 matched tuple

`meta` map	Groovy Map containing sample information about the combined set of files e.g. `[ id:'combined' ]`
`*_matched.txt` file	A txt file containing only the samples that match with each other `*matched.txt`

#4 corr_matrix tuple

`meta` map	Groovy Map containing sample information about the combined set of files e.g. `[ id:'combined' ]`
`*_corr_matrix.txt` file	A text file containing the correlation matrix between each sample `*corr_matrix.txt`

#5 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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:59:05 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fngscheckmate%2Fvafncm/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ngscheckmate/vafncm/blobs/sha256:b20c2f9cd15b220286c5247dc47c940c6f55440436a24157622ad9af7a4716ce
Size	3.6 KB
Checksum	sha256:b20c2f9cd15b220286c5247dc47c940c6f55440436a24157622ad9af7a4716ce
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:59:05 (UTC)		1	3.6 KB	-