make-singlechromfastq/bam2singlechromfastq.cwl

   1 $namespaces:
   2  s: https://schema.org/
   3  edam: http://edamontology.org/
   4  arv: "http://arvados.org/cwl#"
   5 s:codeRepository: https://github.com/arvados/arvados-tutorial
   6 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
   7 cwlVersion: v1.1
   8 class: CommandLineTool
   9 label: Convert one chromosome of bam to fastqs
  10 requirements:
  11   ShellCommandRequirement: {}
  12 hints:
  13   DockerRequirement:
  14     dockerPull: curii/bwa-samtools
  15   ResourceRequirement:
  16     ramMin: 20000
  17     coresMin: 4
  18   arv:RuntimeConstraints:
  19     keep_cache: 9216
  20     outputDirType: keep_output_dir
  21   SoftwareRequirement:
  22     packages:
  23       Samtools:
  24         specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
  25         version: [ "1.10" ]
  26 inputs:
  27   bam:
  28     type: File
  29     #format: edam:format_2572 # BAM
  30     label: Alignments in BAM format
  31     secondaryFiles: [.bai]
  32   sample:
  33     type: string
  34     label: Sample name
  35   chrom:
  36     type: string
  37     label: Chromosome name
  38 outputs:
  39   fastq1:
  40     type: File
  41     #format: edam:format_1930 # FASTQ
  42     label: One of set of pair-end FASTQs (R1)
  43     outputBinding:
  44       glob: "*_1.fastq.gz"
  45   fastq2:
  46     type: File
  47     #format: edam:format_1930 # FASTQ
  48     label: One of set of pair-end FASTQs (R2)
  49     outputBinding:
  50       glob: "*_2.fastq.gz"
  51 baseCommand: [samtools, view]
  52 arguments:
  53   - "-b"
  54   - $(inputs.bam)
  55   - $(inputs.chrom)
  56   - shellQuote: false
  57     valueFrom: "|"
  58   - "samtools"
  59   - "sort"
  60   - "-n"
  61   - "-"
  62   - shellQuote: false
  63     valueFrom: "|"
  64   - "samtools"
  65   - "fastq"
  66   - "-@"
  67   - $(runtime.cores)
  68   - "-"
  69   - "-N"
  70   - prefix: "-0"
  71     valueFrom: "/dev/null"
  72   - prefix: "-s"
  73     valueFrom: "/dev/null"
  74   - prefix: "-1"
  75     valueFrom: $(inputs.sample)_1.fastq.gz
  76   - prefix: "-2"
  77     valueFrom: $(inputs.sample)_2.fastq.gz