cwl/bwamem-samtools-view.cwl

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