nf-core/shapeit5/switch @ 0.0.0-6c4ed3a
Summary
Program to compute switch error rate and genotyping error rate given simulated or trio data.
Get started
Add the following snippet to your workflow script to include this module.
include { SHAPEIT5_SWITCH } from 'nf-core/shapeit5/switch'
License
MIT License
Name
|
SHAPEIT5_SWITCH |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
estimate
file
|
Imputed data. *.{vcf,bcf,vcf.gz,bcf.gz}
|
estimate_index
file
|
Index file of the freq VCF/BCF file. *.{vcf,bcf,vcf.gz,bcf.gz}
|
region
string
|
Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). chrXX:leftBufferPosition-rightBufferPosition
|
pedigree
file
|
Pedigree information in the following format: offspring father mother. *.{txt, tsv}
|
truth
file
|
Validation dataset called at the same positions as the imputed file. *.{vcf,bcf,vcf.gz,bcf.gz}
|
truth_index
file
|
Index file of the truth VCF/BCF file. *.{vcf,bcf,vcf.gz,bcf.gz}
|
freq
file
|
File containing allele frequencies at each site. *.{vcf,bcf,vcf.gz,bcf.gz}
|
freq_index
file
|
Index file of the freq VCF/BCF file. *.{vcf.gz.csi,bcf.gz.csi}
|
errors
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt.gz
file
|
Estimates errors from the phased file. *.txt.gz
|
versions_shapeit5
tuple
${task.process}
string
|
The name of the process |
|---|---|
shapeit5
string
|
The name of the tool |
SHAPEIT5_switch | sed "5!d;s/^.*Version *: //; s/ .*$//"
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 15:45:09 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fshapeit5%2Fswitch/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/shapeit5/switch/blobs/sha256:989506cd5ea37a9f2b9c3f99280c7963ce915d2c356da891ea4402d3f7d9355c |
| Size | 3.4 KB |
| Checksum | sha256:989506cd5ea37a9f2b9c3f99280c7963ce915d2c356da891ea4402d3f7d9355c |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:45:09 (UTC) | 3 | 3.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:31:01 (UTC) | 3 | 3.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:37:36 (UTC) | 3 | 3.4 KB |