rnaseq-engineering/tasks/fastqc.wdl

task fastqc {
  File read1
  File read2
  String docker
  String read1name=sub(basename(read1),"\\.\\S+$", "")
  String read2name=sub(basename(read2),"\\.\\S+$", "")
  String cluster
  String disk_size

  command <<<
    set -o pipefail
    set -e
    nt=$(nproc)
    fastqc -t $nt -o ./ ${read1}
    fastqc -t $nt -o ./ ${read2}
  >>>

  runtime {
    docker:docker
    cluster: cluster
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }
  output {
    File read1_html="${read1name}_fastqc.html"
    File read1_zip="${read1name}_fastqc.zip"
    File read2_html="${read2name}_fastqc.html"
    File read2_zip="${read1name}_fastqc.zip"
  }
}