Nextflow Registry | nf-core/gangstr@0.0.0-0c7146d

nf-core/gangstr @ 0.0.0-0c7146d

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

gangstr STR bam cram vcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

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

include { GANGSTR } from 'nf-core/gangstr'

MIT License

Process

`Name`	`GANGSTR`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`alignment_files` file	Alignment files
`alignment_indices` file	The index/indices of the BAM/CRAM file(s) `*.{bai,crai}`
`ref_regions` file	A reference set of regions to genotype in a BED-like format. The file should have following columns: The name of the chromosome on which the STR is located The start position of the STR on its chromosome The end position of the STR on its chromosome The motif length The repeat motif `*.bed`

`fasta` file	The reference FASTA file `*.{fasta,fa}`

`fasta_fai` file	The index of the reference FASTA file `*.fai`

Output 4 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	The resulting VCF file containing the genotypes `*.vcf.gz`

#2 index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz.tbi` file	The resulting index of the VCF file containing the genotypes `*.vcf.gz.tbi`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

#4 samplestats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.samplestats.tab` file	A tab-delimited file containing statistics for each sample `*.tab`

Tool	Description	Homepage
gangstr	GangSTR is a tool for genome-wide profiling tandem repeats from short reads.	https://github.com/gymreklab/GangSTR

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:40:31 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgangstr/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gangstr/blobs/sha256:b5d021d7eaec2f7d37e5edcd4f0c304d7bfb0b3ce14fde09f71a374b9615bfca
Size	3.3 KB
Checksum	sha256:b5d021d7eaec2f7d37e5edcd4f0c304d7bfb0b3ce14fde09f71a374b9615bfca
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:40:31 (UTC)		1	3.3 KB	-