make-singlechromfastq/scatter-bam2singlechromfastq-wf.cwl

   1 $namespaces:
   2  s: https://schema.org/
   3  edam: http://edamontology.org/
   4 s:codeRepository: https://github.com/arvados/arvados-tutorial
   5 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
   6 cwlVersion: v1.1
   7 class: Workflow
   8 label: Scatter to convert one chromosome of bam to fastqs
   9 requirements:
  10   ScatterFeatureRequirement: {}
  11
  12 inputs:
  13   bams:
  14     type:
  15       type: array
  16       items: File
  17     format: edam:format_2572 # BAM
  18     secondaryFiles: [.bai]
  19     label: Alignments in BAM format
  20   samples:
  21     type:
  22       type: array
  23       items: string
  24     label: Sample names
  25   chrom:
  26     type: string
  27     label: Chromosome name
  28
  29 outputs:
  30   fastq1s:
  31     type:
  32       type: array
  33       items: File
  34     format: edam:format_1930 # FASTQ
  35     label: One of set of pair-end FASTQs (R1)
  36     outputSource: bam2singlechromfastq/fastq1
  37   fastq2s:
  38     type:
  39       type: array
  40       items: File
  41     format: edam:format_1930 # FASTQ
  42     label: One of set of pair-end FASTQs (R2)
  43     outputSource: bam2singlechromfastq/fastq2
  44
  45 steps:
  46   bam2singlechromfastq:
  47     run: bam2singlechromfastq.cwl
  48     scatter: [bam, sample]
  49     scatterMethod: dotproduct
  50     in:
  51       bam: bams
  52       sample: samples
  53       chrom: chrom
  54     out: [fastq1, fastq2]