blog-examples/debugging/star-index/STAR-index-broken.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
   9 inputs:
  10
  11   InputFiles:
  12     format: http://edamontology.org/format_1930
  13     type: File[]
  14     inputBinding:
  15       prefix: "--genomeFastaFiles"
  16
  17   IndexName:
  18     type: string
  19     inputBinding:
  20       prefix: "--genomeDir"
  21       valueFrom: ./$(self)
  22
  23 #Optional Inputs
  24
  25   Gtf:
  26     type: File?
  27     inputBinding:
  28       prefix: "--sjdbGTFfile"
  29
  30   Overhang:
  31     type: int?
  32     inputBinding:
  33       prefix: "--sjdbOverhang"
  34
  35   Junctions:
  36     type: File?
  37     inputBinding:
  38       prefix: "--sjdbFileChrStartEnd"
  39
  40   GenomeSize:
  41     type: int?
  42     inputBinding:
  43       prefix: "--genomeSAindexNbases"
  44
  45   GenomeBits:
  46     type: int?
  47     inputBinding:
  48       prefix: "--genomeChrBinNbits"
  49
  50 baseCommand: [STAR, --runMode, genomeGenerate]
  51
  52 arguments: [--runThreadN, $(runtime.cores)]
  53
  54 outputs:
  55   indexes:
  56     type: Directory
  57     outputBinding:
  58       glob: ./$(inputs.IndexName)/