WGS-processing/cwl/helper/bwamem-samtools-view.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Aligning fastqs with BWA
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7   cwltool: "http://commonwl.org/cwltool#"
   8
   9 requirements:
  10   DockerRequirement:
  11     dockerPull: curii/bwa-samtools-picard
  12   ShellCommandRequirement: {}
  13   ResourceRequirement:
  14     ramMin: 50000
  15     coresMin: 16
  16
  17 hints:
  18   arv:RuntimeConstraints:
  19     keep_cache: 1024
  20     outputDirType: keep_output_dir
  21
  22 inputs:
  23   reference:
  24     type: File
  25     secondaryFiles:
  26       - .amb
  27       - .ann
  28       - .bwt
  29       - .pac
  30       - .sa
  31       - .fai
  32       - ^.dict
  33   fastq1: File
  34   fastq2: File
  35   sample: string
  36
  37 stdout: $(inputs.sample).bam
  38
  39 outputs:
  40   bam:
  41     type: File
  42     outputBinding:
  43       glob: "*bam"
  44
  45 arguments:
  46   - /bwa-0.7.17/bwa
  47   - mem
  48   - -M
  49   - -t
  50   - $(runtime.cores)
  51   - $(inputs.reference)
  52   - -R
  53   - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
  54   - -c
  55   - '250'
  56   - $(inputs.fastq1)
  57   - $(inputs.fastq2)
  58   - shellQuote: false
  59     valueFrom: '|'
  60   - samtools
  61   - view
  62   - -@
  63   - $(runtime.cores)
  64   - -b
  65   - -S
  66   - shellQuote: false
  67     valueFrom: '-'