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

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

Tools for population-scale genotyping using pangenome graphs.

variant vcf bam cram pangenome

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @zachary-foster

Maintainers: @zachary-foster

Tools for population-scale genotyping using pangenome graphs.

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

include { GRAPHTYPER_GENOTYPE } from 'nf-core/graphtyper/genotype'

MIT License

Process

`Name`	`GRAPHTYPER_GENOTYPE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`bam` file	BAM/CRAM file `*.{bam,cram}`
`bai` file	BAM index file. This is automatically found base on BAM input file name `*.{bai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`ref` file	Reference fasta file `*.{fa, fasta, fas}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`ref_fai` file	Reference index file. This is automatically found based on reference input file name. `*.{.fai}`

`region_file` file	File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or `--region` (in ext.args) must be specified. `*`

Output 3 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`results//.vcf.gz.tbi` file	VCF index file `*.{vcf.gz.tbi}`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`results//.vcf.gz` file	VCF file with genotyped variants `*.{vcf.gz}`

#3 versions

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

Tool	Description	Homepage
graphtyper	A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.	https://github.com/DecodeGenetics/graphtyper

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:45:19 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgraphtyper%2Fgenotype/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/graphtyper/genotype/blobs/sha256:f85a2f280151def259c277515e668a5aa221a987884e06d8cba3110ce39fed8e
Size	3.3 KB
Checksum	sha256:f85a2f280151def259c277515e668a5aa221a987884e06d8cba3110ce39fed8e
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:45:19 (UTC)		1	3.3 KB	-