nf-core/beagle5/beagle @ 0.0.0-6c4ed3a
Summary
Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers.
Get started
Add the following snippet to your workflow script to include this module.
include { BEAGLE5_BEAGLE } from 'nf-core/beagle5/beagle'
License
MIT License
Name
|
BEAGLE5_BEAGLE |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
vcf
file
|
target VCF input file to be imputed and or phased *.{vcf,vcf.gz}
|
vcf_index
file
|
target VCF input file index *.{vcf,vcf.gz}.{tbi,csi}
|
refpanel
file
|
target reference panel *.{vcf,vcf.gz}
|
refpanel_index
file
|
target reference panel index *.{vcf,vcf.gz}.{tbi,csi}
|
genmap
file
|
a PLINK format genetic map with cM units *.{map,map.gz,map.zip}
|
exclsamples
file
|
text file containing samples one sample per line to be excluded from the analysis *.*
|
exclmarkers
file
|
text file containing markers one marker per line to be excluded from the analysis *.*
|
region
string
|
Region to perform imputation (chr)?\d*:\d*-\d*
|
log
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.log
file
|
a summary of the analysis that includes the Beagle version, the command line arguments, and compute time. *.log
|
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.vcf.gz
file
|
bgzip compressed VCF file that contains phased non missing genotypes for all non reference samples *.vcf.gz
|
versions_beagle
tuple
${task.process}
string
|
The name of the process |
|---|---|
beagle
string
|
The name of the tool |
beagle 2>&1 | sed -n 's/.*version \([^)]*\).*/\1/p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| beagle5 | Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. | https://faculty.washington.edu/browning/beagle/beagle.html |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:05:23 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbeagle5%2Fbeagle/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/beagle5/beagle/blobs/sha256:5290ba818a6b2835801e1efcfcb6827204acdfecb4c2a16cfc3d246a768749ae |
| Size | 3.3 KB |
| Checksum | sha256:5290ba818a6b2835801e1efcfcb6827204acdfecb4c2a16cfc3d246a768749ae |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:05:23 (UTC) | 3 | 3.3 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:03:27 (UTC) | 4 | 3.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:46:38 (UTC) | 4 |