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nf-core/ngscheckmate/vafncm @ 0.0.0-3fc6d40

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: 0.0.0-6c4ed3a
Total downloads: 9
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 0.0.0-3fc6d40
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 22 Apr 2026 15:23:38 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fngscheckmate%2Fvafncm/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ngscheckmate/vafncm/blobs/sha256:8ac925c4d35fa140b4838453224b3952a49ec21c9f756aad3cb4161ca8eb1579
Size 3.6 KB
Checksum sha256:8ac925c4d35fa140b4838453224b3952a49ec21c9f756aad3cb4161ca8eb1579
Downloads 2
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:33:14 (UTC) 4 3.6 KB
0.0.0-3fc6d40 22 Apr 2026 15:23:38 (UTC) 2 3.6 KB
0.0.0-0c7146d 08 Apr 2026 19:21:31 (UTC) 3 3.6 KB