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

nf-core/ngscheckmate/patterngenerator @ 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_PATTERNGENERATOR } from 'nf-core/ngscheckmate/patterngenerator'

License

MIT License

Process

`Name`	`NGSCHECKMATE_PATTERNGENERATOR`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information about the bed file e.g. `[ id:'test', single_end:false ]`
`bed` file	BED file containing population-level SNPs to use `*.bed`

#2 tuple

`meta2` map	Groovy Map containing sample information about the fasta genome e.g. `[ id:'test', single_end:false ]`
`fasta` file	Genome fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bowtie_index` directory	Folder of Bowtie genome index files

Output 2 channels

#1 pt tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.pt` file	Generated binary pattern file, containing FASTQ strings to match from within raw data `*.pt`

#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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:59:03 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fngscheckmate%2Fpatterngenerator/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ngscheckmate/patterngenerator/blobs/sha256:91ff1ee250e7755e4f93c341ad4c7b2678ad0cb65c6cac1a6bcea9cc815b8949
Size	2.7 KB
Checksum	sha256:91ff1ee250e7755e4f93c341ad4c7b2678ad0cb65c6cac1a6bcea9cc815b8949
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:59:03 (UTC)		1	2.7 KB	-