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

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

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: 7

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:33:13 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fngscheckmate%2Fpatterngenerator/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ngscheckmate/patterngenerator/blobs/sha256:53f5529b8905b0123f5fb50bfaaf1bb063b53b25dd7d7efd90f7e6a484be71a2
Size	2.7 KB
Checksum	sha256:53f5529b8905b0123f5fb50bfaaf1bb063b53b25dd7d7efd90f7e6a484be71a2
Downloads	2

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:33:13 (UTC)	2	2.7 KB
0.0.0-3fc6d40	22 Apr 2026 15:23:37 (UTC)	3	2.7 KB
0.0.0-0c7146d	08 Apr 2026 19:21:29 (UTC)	2	2.7 KB