mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
01d6d4c286
* Creation of Glimpse Chunk Add sub tools chunk with configuration and needed files for unitest. * Code linting correction * Prettier ran Newline deleted in nextflow.config * New final line and white spaces * Change Pytest.yml to work as a subtool. * Control for the parameters deleted. Control for the size/count of the window and buffer not needed. They have some defaults value. * Changed the different recommended part by @nvnieuwk Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
52 lines
1.6 KiB
YAML
52 lines
1.6 KiB
YAML
name: "glimpse_chunk"
|
|
description: Defines chunks where to run imputation
|
|
keywords:
|
|
- chunk
|
|
- imputation
|
|
tools:
|
|
- "glimpse":
|
|
description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies."
|
|
homepage: "https://odelaneau.github.io/GLIMPSE"
|
|
documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
|
|
tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
|
|
doi: "10.1038/s41588-020-00756-0"
|
|
licence: "['MIT']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
|
|
- input:
|
|
type: file
|
|
description: |
|
|
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).
|
|
pattern: "*.{vcf,bcf}"
|
|
|
|
- region:
|
|
type: string
|
|
description: |
|
|
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.
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
- txt:
|
|
type: file
|
|
description: Tab delimited output txt file containing buffer and imputation regions.
|
|
pattern: "*.{txt}"
|
|
|
|
authors:
|
|
- "@louislenezet"
|