Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
meta is associated to the PLINK native file input
bed{:bash}
:file
PLINK binary biallelic genotype table file
*.{bed}
bim{:bash}
:file
PLINK extended MAP file
*.{bim}
fam{:bash}
:file
PLINK sample information file
*.{fam}
meta2{:bash}
:map
Groovy Map containing sample information,
e.g. [ id:‘test’, single_end:false ]
meta2 is associated to VCF file input
vcf{:bash}
:file
Variant calling file (vcf)
*.{vcf}
meta3{:bash}
:map
Groovy Map containing sample information,
e.g. [ id:‘test’, single_end:false ]
meta3 is associated to BCF file input
bcf{:bash}
:file
PLINK variant information + sample ID + genotype call binary file
*.{bcf}
meta4{:bash}
:map
Groovy Map containing sample information,
e.g. [ id:‘test’, single_end:false ]
meta4 is associated to phenotype file input
phe{:bash}
:file
PLINK file containing phenotype information. This phenotype information can be read from the third column with the —pheno option or from a specific column with the —pheno-name option
*.{phe}
Output
name:type
description
pattern
assoc{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.assoc{:bash}
:file
PLINK GWAS association file
*.{assoc}
log{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log{:bash}
:file
PLINK GWAS association log file
*.{log}
nosex{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.nosex{:bash}
:file
PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option —allow-no-sex
*.{nosex}
versions_plink{:bash}
${task.process}{:bash}
:string
The name of the process
plink{:bash}
:string
The name of the tool
plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'{:bash}
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The name of the process
plink{:bash}
:string
The name of the tool
plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'{:bash}
: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.
