cwl/fastqc.cwl

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