nf-core/glimpse2/ligate @ 0.0.0-0c7146d
Summary
Ligatation of multiple phased BCF/VCF files into a single whole chromosome file. GLIMPSE2 is run in chunks that are ligated into chromosome-wide files maintaining the phasing.
Get started
Add the following snippet to your workflow script to include this module.
include { GLIMPSE2_LIGATE } from 'nf-core/glimpse2/ligate'
License
MIT License
Process
Name
|
GLIMPSE2_LIGATE |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input_list
file
|
VCF/BCF file containing genotype probabilities (GP field). *.{vcf,bcf,vcf.gz,bcf.gz}
|
input_index
file
|
Index file of the input VCF/BCF file containing genotype likelihoods. *.{csi,tbi}
|
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 ligated (phased) file in VCF/BCF format. *.{vcf,bcf,vcf.gz,bcf.gz}
|
#2
versions_glimpse2
tuple
${task.process}
string
|
The name of the process |
|---|---|
glimpse2
string
|
The name of the tool |
GLIMPSE2_ligate --help | grep -oE 'v[0-9.]+' | cut -c2-
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| glimpse2 | GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies. | https://odelaneau.github.io/GLIMPSE |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:44:52 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fglimpse2%2Fligate/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/glimpse2/ligate/blobs/sha256:4635a3d561baabac17ec214e25bf98ebe0de56f9a5206485c48731ad7d6dcbdb |
| Size | 3.1 KB |
| Checksum | sha256:4635a3d561baabac17ec214e25bf98ebe0de56f9a5206485c48731ad7d6dcbdb |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:44:52 (UTC) | 1 | 3.1 KB | - |