cwl/bwamem-samtools-view-org.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Realigning fastqs and converting output to bam
   4 $namespaces:
   5   arv: "http://arvados.org/cwl#"
   6   cwltool: "http://commonwl.org/cwltool#"
   7
   8 requirements:
   9   DockerRequirement:
  10     dockerPull: curii/bwa-samtools-picard
  11   ShellCommandRequirement: {}
  12   ResourceRequirement:
  13     ramMin: 26000
  14     coresMin: 16
  15
  16 hints:
  17   arv:RuntimeConstraints:
  18     outputDirType: keep_output_dir
  19
  20 inputs:
  21   reference:
  22     type: File
  23     secondaryFiles:
  24       - .amb
  25       - .ann
  26       - .bwt
  27       - .pac
  28       - .sa
  29       - .fai
  30       - ^.dict
  31   fastq1: File
  32   fastq2: File
  33   sample: string
  34
  35 stdout: $(inputs.sample).bam
  36
  37 outputs:
  38   bam:
  39     type: File
  40     outputBinding:
  41       glob: "*bam"
  42
  43 arguments:
  44   - /bwa-0.7.17/bwa
  45   - mem
  46   - -M
  47   - -t
  48   - $(runtime.cores)
  49   - $(inputs.reference)
  50   - -R
  51   - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
  52   - -c
  53   - '250'
  54   - $(inputs.fastq1)
  55   - $(inputs.fastq2)
  56   - shellQuote: false
  57     valueFrom: '|'
  58   - samtools
  59   - view
  60   - -@
  61   - $(runtime.cores)
  62   - -b
  63   - -S
  64   - shellQuote: false
  65     valueFrom: '-'