WGS-processing/cwl/helper/bwamem-samtools-view.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: 50000
  14     coresMin: 16
  15
  16 hints:
  17   arv:RuntimeConstraints:
  18     keep_cache: 1024
  19     outputDirType: keep_output_dir
  20
  21 inputs:
  22   reference:
  23     type: File
  24     secondaryFiles:
  25       - .amb
  26       - .ann
  27       - .bwt
  28       - .pac
  29       - .sa
  30       - .fai
  31       - ^.dict
  32   fastq1: File
  33   fastq2: File
  34   sample: string
  35
  36 stdout: $(inputs.sample).bam
  37
  38 outputs:
  39   bam:
  40     type: File
  41     outputBinding:
  42       glob: "*bam"
  43
  44 arguments:
  45   - /bwa-0.7.17/bwa
  46   - mem
  47   - -M
  48   - -t
  49   - $(runtime.cores)
  50   - $(inputs.reference)
  51   - -R
  52   - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
  53   - -c
  54   - '250'
  55   - $(inputs.fastq1)
  56   - $(inputs.fastq2)
  57   - shellQuote: false
  58     valueFrom: '|'
  59   - samtools
  60   - view
  61   - -@
  62   - $(runtime.cores)
  63   - -b
  64   - -S
  65   - shellQuote: false
  66     valueFrom: '-'