lesson3/answers/featureCounts.cwl

   1 ### 1. File header
   2 cwlVersion: v1.2
   3 class: CommandLineTool
   4
   5 ### 2. Command line tool inputs
   6 inputs:
   7   gtf: File
   8   counts_input_bam: File
   9
  10 ### 3. Specifying the program to run
  11 baseCommand: featureCounts
  12
  13 ### 4. Command arguments
  14 arguments: [-T, $(runtime.cores),
  15             -a, $(inputs.gtf),
  16             -o, featurecounts.tsv,
  17             $(inputs.counts_input_bam)]
  18
  19 ### 5. Outputs section
  20 outputs:
  21   featurecounts:
  22     type: File
  23     outputBinding:
  24       glob: featurecounts.tsv
  25
  26 ### 6. Running in a container
  27 hints:
  28   DockerRequirement:
  29     dockerPull: quay.io/biocontainers/subread:1.5.0p3--0