blog-examples/debugging/star-index/STAR-index.cwl

   1 #!/usr/bin/env cwl-runner
   2 cwlVersion: v1.0
   3 class: CommandLineTool
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
   8   ResourceRequirement:
   9     coresMin: 2
  10     ramMin: 12000
  11
  12 inputs:
  13
  14   InputFiles:
  15     format: http://edamontology.org/format_1930
  16     type: File[]
  17     inputBinding:
  18       prefix: "--genomeFastaFiles"
  19
  20   IndexName:
  21     type: string
  22     inputBinding:
  23       prefix: "--genomeDir"
  24       valueFrom: ./$(self)
  25
  26 #Optional Inputs
  27
  28   Gtf:
  29     type: File?
  30     inputBinding:
  31       prefix: "--sjdbGTFfile"
  32
  33   Overhang:
  34     type: int?
  35     inputBinding:
  36       prefix: "--sjdbOverhang"
  37
  38   Junctions:
  39     type: File?
  40     inputBinding:
  41       prefix: "--sjdbFileChrStartEnd"
  42
  43   GenomeSize:
  44     type: int?
  45     inputBinding:
  46       prefix: "--genomeSAindexNbases"
  47
  48   GenomeBits:
  49     type: int?
  50     inputBinding:
  51       prefix: "--genomeChrBinNbits"
  52
  53 baseCommand: [STAR, --runMode, genomeGenerate]
  54
  55 arguments: [--runThreadN, $(runtime.cores)]
  56
  57 outputs:
  58   indexes:
  59     type: Directory
  60     outputBinding:
  61       glob: ./$(inputs.IndexName)/