Nextflow Registry | nf-core/ngscheckmate/fastq@0.0.0-3fc6d40

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

Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module.

ngscheckmate matching snp qc

Latest version: 0.0.0-6c4ed3a

Total downloads: 3

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 vaf files for individual fastq file(s), ready for the vafncm module.

Get started

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

include { NGSCHECKMATE_FASTQ } from 'nf-core/ngscheckmate/fastq'

License

MIT License

Process

`Name`	`NGSCHECKMATE_FASTQ`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information about the fastq files e.g. `[ id:'test', single_end:false ]`
`reads` file	Raw fastq files for one sample, single or paired end. `*.{fastq.gz}`

#2 tuple

`meta2` file	Groovy Map containing sample information about the NGSCheckMate SNP pt file e.g. `[ id:'test', single_end:false ]`
`snp_pt` file	PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate's github repository. `*.{pt}`

Output 2 channels

#1 vaf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.vaf` file	Text file containing reference/alt allele depth for each SNP position contained in the PT file. `*.{vaf}`

#2 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 15:23:34 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fngscheckmate%2Ffastq/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ngscheckmate/fastq/blobs/sha256:0bb517d79ae95e63d2d40c85b47cde35020bf1b934d213cff130e0cfdbdf40c9
Size	3.1 KB
Checksum	sha256:0bb517d79ae95e63d2d40c85b47cde35020bf1b934d213cff130e0cfdbdf40c9
Downloads	1

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:33:10 (UTC)	1	3.1 KB
0.0.0-3fc6d40	22 Apr 2026 15:23:34 (UTC)	1	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:21:25 (UTC)	1	3.0 KB