WGS-processing/cwl/helper/samtools-index.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Index BAM
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: curii/bwa-samtools-picard
   8   InitialWorkDirRequirement:
   9     listing:
  10       - $(inputs.bam)
  11
  12 hints:
  13   arv:RuntimeConstraints:
  14     outputDirType: keep_output_dir
  15   SoftwareRequirement:
  16     packages:
  17       Samtools:
  18         specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
  19         version: [ "1.10" ]
  20
  21 inputs:
  22   bam:
  23     type: File
  24     format: edam:format_2572 # BAM
  25     label: Sorted BAM with labeled duplicates
  26
  27 outputs:
  28   indexedbam:
  29     type: File
  30     format: edam:format_2572 # BAM
  31     label: Indexed sorted BAM with labeled duplicates
  32     outputBinding:
  33       glob: "*bam"
  34     secondaryFiles:
  35       - .bai
  36
  37 baseCommand: samtools
  38
  39 arguments:
  40   - index
  41   - $(inputs.bam.basename)
  42
  43 s:codeRepository: https://github.com/arvados/arvados-tutorial
  44 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  45
  46 $namespaces:
  47  s: https://schema.org/
  48  edam: http://edamontology.org/
  49  arv: "http://arvados.org/cwl#"
  50  cwltool: "http://commonwl.org/cwltool#"
  51
  52 $schemas:
  53  - https://schema.org/version/latest/schema.rdf
  54  - http://edamontology.org/EDAM_1.18.owl