nf-core/graphtyper/genotype @ 0.0.0-6c4ed3a
Summary
Tools for population-scale genotyping using pangenome graphs.
Get started
Add the following snippet to your workflow script to include this module.
include { GRAPHTYPER_GENOTYPE } from 'nf-core/graphtyper/genotype'
License
MIT License
Name
|
GRAPHTYPER_GENOTYPE |
|---|
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}
|
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
ref
file
|
Reference fasta file *.{fa, fasta, fas}
|
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 *
|
|---|
tbi
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
results/*/*.vcf.gz.tbi
file
|
VCF index file *.{vcf.gz.tbi}
|
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
results/*/*.vcf.gz
file
|
VCF file with genotyped variants *.{vcf.gz}
|
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:21:57 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgraphtyper%2Fgenotype/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/graphtyper/genotype/blobs/sha256:5786af92b4e50dd86ce964e8cd58bb21d249a702a895cdfcdc6d2dd62c29c627 |
| Size | 3.3 KB |
| Checksum | sha256:5786af92b4e50dd86ce964e8cd58bb21d249a702a895cdfcdc6d2dd62c29c627 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:21:57 (UTC) | 3 | 3.3 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:14:25 (UTC) | 3 | 3.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:06:53 (UTC) | 3 | 3.3 KB |