nf-core_modules/modules/plink2/extract/meta.yml

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name: plink2_extract
description: Subset plink pfiles with a text file of variant identifiers
keywords:
- plink2
- extract
tools:
- plink2:
description: |
Whole genome association analysis toolset, designed to perform a range
of basic, large-scale analyses in a computationally efficient manner
homepage: http://www.cog-genomics.org/plink/2.0/
documentation: http://www.cog-genomics.org/plink/2.0/general_usage
tool_dev_url: None
doi: "10.1186/s13742-015-0047-8"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- pgen:
type: file
description: PLINK 2 binary genotype table
pattern: "*.{pgen}"
- psam:
type: file
description: PLINK 2 sample information file
pattern: "*.{psam}"
- pvar:
type: file
description: PLINK 2 variant information file
pattern: "*.{pvar}"
- variants:
type: file
description: A text file containing variant identifiers to keep (one per line)
pattern: "*.{keep}"
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"
- extract_pgen:
type: file
description: PLINK 2 binary genotype table, containing extracted variants
pattern: "*.{pgen}"
- extract_psam:
type: file
description: PLINK 2 sample information file associated with the extracted data
pattern: "*.{psam}"
- extract_pvar:
type: file
description: PLINK 2 variant information file, containing extracted variants
pattern: "*.{pvar.zst}"
authors:
- "@nebfield"