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

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Sorting BAM file
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: curii/bwa-samtools-picard
   8   ShellCommandRequirement: {}
   9   ResourceRequirement:
  10     ramMin: 20000
  11     coresMin: 4
  12
  13 hints:
  14   arv:RuntimeConstraints:
  15     keep_cache: 9216
  16     outputDirType: keep_output_dir
  17   SoftwareRequirement:
  18     packages:
  19       Samtools:
  20         specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
  21         version: [ "1.10" ]
  22
  23 inputs:
  24   bam:
  25     type: File
  26     format: edam:format_2572 # BAM
  27     label: Alignments in BAM format
  28   sample:
  29     type: string
  30     label: Sample Name
  31
  32 outputs:
  33   sortedbam:
  34     type: File
  35     format: edam:format_2572 # BAM
  36     label: Sorted BAM
  37     outputBinding:
  38       glob: "*sorted.bam"
  39
  40 baseCommand: samtools
  41
  42 arguments:
  43   - sort
  44   - -@
  45   - $(runtime.cores)
  46   - $(inputs.bam.path)
  47   - -m
  48   - '2G'
  49   - -o
  50   - $(inputs.sample).sorted.bam
  51
  52 s:codeRepository: https://github.com/arvados/arvados-tutorial
  53 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  54
  55 $namespaces:
  56  s: https://schema.org/
  57  edam: http://edamontology.org/
  58  arv: "http://arvados.org/cwl#"
  59  cwltool: "http://commonwl.org/cwltool#"
  60
  61 $schemas:
  62  - https://schema.org/version/latest/schema.rdf
  63  - http://edamontology.org/EDAM_1.18.owl