nf-core/shapeit5/ligate @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:45:05 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fshapeit5%2Fligate/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/shapeit5/ligate/blobs/sha256:528513a5730205e8628658b1b60fb9edcb6742e6779369d8f9bcf9ae77757901 |
| Size | 3.2 KB |
| Checksum | sha256:528513a5730205e8628658b1b60fb9edcb6742e6779369d8f9bcf9ae77757901 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:45:05 (UTC) | 3 | 3.2 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:30:57 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:37:30 (UTC) | 3 | 3.1 KB |