nf-core/shapeit5/ligate @ 0.0.0-0c7146d
Summary
Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.
Get started
Add the following snippet to your workflow script to include this module.
include { SHAPEIT5_LIGATE } from 'nf-core/shapeit5/ligate'
License
MIT License
Process
Name
|
SHAPEIT5_LIGATE |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input_list
file
|
VCF/BCF files containing genotype probabilities (GP field). The files should be ordered by genomic position. *.{vcf,bcf,vcf.gz,bcf.gz}
|
input_list_index
file
|
VCF/BCF files index. *.csi
|
suffix_
string
|
Output format *.{vcf,bcf,vcf.gz,bcf.gz}
|
|---|
Output
2 channels
#1
merged_variants
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.{vcf,bcf,vcf.gz,bcf.gz}
file
|
Output VCF/BCF file for the merged regions. Phased information (HS field) is updated accordingly for the full region. *.{vcf,bcf,vcf.gz,bcf.gz}
|
#2
versions_shapeit5
tuple
${task.process}
string
|
The name of the process |
|---|---|
shapeit5
string
|
The name of the tool |
SHAPEIT5_ligate | sed "5!d;s/^.*Version *: //; s/ .*$//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| shapeit5 | Fast and accurate method for estimation of haplotypes (phasing) | https://odelaneau.github.io/shapeit5/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:13:38 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fshapeit5%2Fligate/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/shapeit5/ligate/blobs/sha256:5aa474e187b70d9e40cf7e4d2647cc9293b5e32956bf79e920a4bf347e60eb7e |
| Size | 3.1 KB |
| Checksum | sha256:5aa474e187b70d9e40cf7e4d2647cc9293b5e32956bf79e920a4bf347e60eb7e |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:13:38 (UTC) | 1 | 3.1 KB | - |