WGS-processing/cwl/helper/fastqc.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Quality check on fastq data using FastQC
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: curii/fastqc
   8   InitialWorkDirRequirement:
   9     listing:
  10       - $(inputs.fastq1)
  11       - $(inputs.fastq2)
  12
  13 inputs:
  14   fastq1: File
  15   fastq2: File
  16
  17 outputs:
  18   out-html:
  19     type: File[]
  20     outputBinding:
  21       glob: "*html"
  22   out-zip:
  23     type: File[]
  24     outputBinding:
  25       glob: "*fastqc.zip"
  26
  27 baseCommand: perl
  28 arguments:
  29   - /FastQC/fastqc
  30   - $(inputs.fastq1.basename)
  31   - $(inputs.fastq2.basename)