cwl/bwamem-samtools-view.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   4 requirements:
   5   DockerRequirement:
   6     dockerPull: curii/bwa-samtools-picard
   7   ShellCommandRequirement: {}
   8   ResourceRequirement:
   9     ramMin: 26000
  10     coresMin: 8
  11
  12 arguments:
  13   - /bwa-0.7.17/bwa
  14   - mem
  15   - -t
  16   - $(runtime.cores)
  17   - $(inputs.reference)
  18   - -R
  19   - "@RG\\tID:sample\\tSM:sample\\tLB:sample\\tPL:ILLUMINA"
  20   - $(inputs.fastq1)
  21   - $(inputs.fastq2)
  22   - shellQuote: false
  23     valueFrom: '|'
  24   - samtools
  25   - view
  26   - -b
  27   - -S
  28   - shellQuote: false
  29     valueFrom: '-'
  30
  31 inputs:
  32   reference:
  33     type: File
  34     secondaryFiles:
  35       - .amb
  36       - .ann
  37       - .bwt
  38       - .pac
  39       - .sa
  40       - .fai
  41       - ^.dict
  42   fastq1: File
  43   fastq2: File
  44   sample: string
  45
  46 stdout: $(inputs.sample).bam
  47
  48 outputs:
  49   bam:
  50     type: File
  51     outputBinding:
  52       glob: "*bam"