lesson4/answers/part2/featureCounts.cwl

   1 cwlVersion: v1.2
   2 class: CommandLineTool
   3
   4 inputs:
   5   gtf: File
   6   counts_input_bam: File
   7
   8 baseCommand: featureCounts
   9
  10 arguments: [-T, $(runtime.cores),
  11             -a, $(inputs.gtf),
  12             -o, featurecounts.tsv,
  13             $(inputs.counts_input_bam)]
  14
  15 outputs:
  16   featurecounts:
  17     type: File
  18       outputBinding:
  19       glob: featurecounts.tsv
  20
  21 hints:
  22   DockerRequirement:
  23     dockerPull: quay.io/biocontainers/subread:1.5.0p3--0