nf-core/glimpse2/chunk @ 0.0.0-6c4ed3a
Summary
Defines chunks where to run imputation
Get started
Add the following snippet to your workflow script to include this module.
include { GLIMPSE2_CHUNK } from 'nf-core/glimpse2/chunk'
License
MIT License
Name
|
GLIMPSE2_CHUNK |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
Target dataset in VCF/BCF format defined at all variable positions. The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). *.{vcf,bcf,vcf.gz,bcf.gz}
|
input_index
file
|
Index file of the input VCF/BCF file containing genotype likelihoods. *.{vcf.gz.csi,bcf.gz.csi}
|
region
string
|
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. |
map
file
|
File containing the genetic map. *.gmap
|
model
string
|
Algorithm model to use: "recursive": Recursive algorithm "sequential": Sequential algorithm (Recommended) "uniform-number-variants": Experimental. Uniform the number of variants in the sequential algorithm {recursive,sequential,uniform-number-variants}
|
|---|
chunk_chr
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt
file
|
Tab delimited output txt file containing buffer and imputation regions. *.{txt}
|
versions_glimpse2
tuple
${task.process}
string
|
The name of the process |
|---|---|
glimpse2
string
|
The name of the tool |
GLIMPSE2_chunk --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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:21:36 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fglimpse2%2Fchunk/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/glimpse2/chunk/blobs/sha256:065125f4f782119a48ea9e613b3fee898d33ee3515f03a31da457423cf17aa7b |
| Size | 3.1 KB |
| Checksum | sha256:065125f4f782119a48ea9e613b3fee898d33ee3515f03a31da457423cf17aa7b |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:21:36 (UTC) | 3 | 3.1 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:14:07 (UTC) | 3 | 3.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:06:22 (UTC) | 2 | 3.1 KB |