Nextflow Registry | nf-core/trgt/genotype@0.0.0-0c7146d

nf-core/trgt/genotype @ 0.0.0-0c7146d

Tandem repeat genotyping from PacBio HiFi data

repeat expansion pacbio genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @Schmytzi @fellen31

Maintainers: @Schmytzi

Tandem repeat genotyping from PacBio HiFi data

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

include { TRGT_GENOTYPE } from 'nf-core/trgt/genotype'

MIT License

Process

`Name`	`TRGT_GENOTYPE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bam` file	Sorted BAM file `*.bam`
`bai` file	Index of the BAM file `*.bam`
`karyotype` string	Karyotype of the sample. Either XX or XY. Defaults to XX if not given

#2 tuple

`meta2` map	Groovy map containing reference information e.g. `[ id: 'genome' ]`
`fasta` file	FASTA reference file `*.{fasta,fa,fna}`

#3 tuple

`meta3` map	Groovy map containing reference information e.g. `[ id: 'genome' ]`
`fai` file	Index for FASTA file `*.fai`

#4 tuple

`meta4` map	Groovy map containing repeat information e.g. `[ id: 'repeats' ]`
`repeats` file	BED file with repeat coordinates `*.bed`

Output 3 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.spanning.bam` file	BAM file with pieces of reads aligning to repeats `*.spanning.bam`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.vcf.gz` file	VCF file with repeat genotypes `*.vcf.gz`

#3 versions_trgt tuple

`${task.process}` string	The name of the process
`trgt` string	The name of the tool
`trgt --version \| sed 's/.* //g'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
trgt	Tandem repeat genotyping and visualization from PacBio HiFi data	https://github.com/PacificBiosciences/trgt

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:19:53 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftrgt%2Fgenotype/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/trgt/genotype/blobs/sha256:69af1677eed3a22e8133f77d2ce0d0c07facb229eda914b61ad2ea2c0dfddfc9
Size	3.2 KB
Checksum	sha256:69af1677eed3a22e8133f77d2ce0d0c07facb229eda914b61ad2ea2c0dfddfc9
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:19:53 (UTC)		1	3.2 KB	-