Groovy Map containing genotype sample information for BCF input
e.g. [ id:‘test’ ]
bcf
:file
PLINK variant information + sample ID + genotype call binary file
*.{bcf,bcf.gz}
meta4
:map
Groovy Map containing phenotype information for --pheno
e.g. [ id:‘test’ ]
The phenotype file can be paired with BED/BIM/FAM, VCF, or BCF genotype inputs
phe
:file
PLINK phenotype file passed with --pheno for BED/BIM/FAM, VCF, or BCF input modes. Phenotypes can be read from the third column by default or from a named column with --pheno-name via module arguments
*.{phe}
Output
name:type
description
pattern
assoc
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{assoc,qassoc}
:file
PLINK GWAS association output file (.assoc for case/control traits, .qassoc for quantitative traits)
*.{assoc,qassoc}
log
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log
:file
PLINK GWAS association log file
*.{log}
nosex
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.nosex
:file
PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option —allow-no-sex
*.{nosex}
versions_plink
${task.process}
:string
The name of the process
plink
:string
The name of the tool
plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
plink
:string
The name of the tool
plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'
:eval
The expression to obtain the version of the tool
Tools
plink
GPL
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
