A simple program to parse Illumina NGS data and check it for quality criteria
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
run_dir{:bash}
:file
Illumina sequencing run directory Can be directory or a compressed tar (tar.gz) of the directory
checkqc_config{:bash}
CheckQC configuration file
*.{yml,yaml}
report{:bash}
CheckQC report in json format
*checkqc_report.json
*checkqc_report.json{:bash}
versions_checkqc{:bash}
${task.process}{:bash}
:string
The name of the process
checkqc{:bash}
The name of the tool
checkqc --version | sed -e "s/checkqc, version //g"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
A simple program to parse Illumina NGS data and check it for quality criteria.
