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: 0.0.0-6c4ed3a

Total downloads: 9

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	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:02:06 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgangstr/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gangstr/blobs/sha256:a429932de8eb1c2d8a22d9b9de40f7d4d61272c462e2f46a0ff76e3846ace83d
Size	3.3 KB
Checksum	sha256:a429932de8eb1c2d8a22d9b9de40f7d4d61272c462e2f46a0ff76e3846ace83d
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:18:02 (UTC)	3	3.3 KB
0.0.0-3fc6d40	22 Apr 2026 15:12:41 (UTC)	3	3.3 KB
0.0.0-0c7146d	08 Apr 2026 19:02:06 (UTC)	3	3.3 KB