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

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Align FASTQs with BWA
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: curii/bwa-samtools
   8   ShellCommandRequirement: {}
   9
  10 hints:
  11   arv:RuntimeConstraints:
  12     keep_cache: 1024
  13     outputDirType: keep_output_dir
  14   ResourceRequirement:
  15     ramMin: 50000
  16     coresMin: 16
  17   SoftwareRequirement:
  18     packages:
  19       BWA:
  20         specs: [ "https://identifiers.org/rrid/RRID:SCR_010910" ]
  21         version: [ "0.7.17" ]
  22       Samtools:
  23         specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
  24         version: [ "1.10" ]
  25
  26 inputs:
  27   reference:
  28     type: File
  29     format: edam:format_1929 # FASTA
  30     label: Reference genome
  31     secondaryFiles:
  32       - .amb
  33       - .ann
  34       - .bwt
  35       - .pac
  36       - .sa
  37       - .fai
  38       - ^.dict
  39   fastq1:
  40     type: File
  41     format: edam:format_1930 # FASTQ
  42     label: One of set of pair-end FASTQs (R1)
  43   fastq2:
  44     type: File
  45     format: edam:format_1930 # FASTQ
  46     label: One of set of pair-end FASTQs (R2)
  47   sample:
  48     type: string
  49     label: Sample Name
  50
  51 stdout: $(inputs.sample).bam
  52
  53 outputs:
  54   bam:
  55     type: File
  56     format: edam:format_2572 # BAM
  57     label: Alignments in BAM format
  58     outputBinding:
  59       glob: "*bam"
  60
  61 arguments:
  62   - /bwa-0.7.17/bwa
  63   - mem
  64   - -M
  65   - -t
  66   - $(runtime.cores)
  67   - $(inputs.reference)
  68   - -R
  69   - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
  70   - -c
  71   - '250'
  72   - $(inputs.fastq1)
  73   - $(inputs.fastq2)
  74   - shellQuote: false
  75     valueFrom: '|'
  76   - samtools
  77   - view
  78   - -@
  79   - $(runtime.cores)
  80   - -b
  81   - -S
  82   - shellQuote: false
  83     valueFrom: '-'
  84
  85 s:codeRepository: https://github.com/arvados/arvados-tutorial
  86 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  87
  88 $namespaces:
  89  s: https://schema.org/
  90  edam: http://edamontology.org/
  91  arv: "http://arvados.org/cwl#"
  92  cwltool: "http://commonwl.org/cwltool#"
  93
  94 #$schemas:
  95 # - https://schema.org/version/latest/schema.rdf
  96 # - http://edamontology.org/EDAM_1.18.owl