Subset plink pfiles with a text file of variant identifiers
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
pgen
:file
PLINK 2 binary genotype table
*.{pgen}
psam
PLINK 2 sample information file
*.{psam}
pvar
PLINK 2 variant information file
*.{pvar}
variants
A text file containing variant identifiers to keep (one per line)
*.{keep}
extract_pgen
*.pgen
PLINK 2 binary genotype table, containing extracted variants
extract_psam
*.psam
PLINK 2 sample information file associated with the extracted data
extract_pvar
*.pvar.zst
PLINK 2 variant information file, containing extracted variants
*.{pvar.zst}
versions_plink2
${task.process}
:string
The name of the process
plink2
The name of the tool
plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//'
:eval
The expression to obtain the version of the tool
versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
