lesson5/answers/featureCounts.cwl

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