lesson3/answers/main.cwl

   1 cwlVersion: v1.2
   2 class: Workflow
   3 label: RNAseq CWL practice workflow
   4
   5 inputs:
   6   fq: File
   7   genome: Directory
   8   gtf: File
   9
  10 steps:
  11   fastqc:
  12     run: bio-cwl-tools/fastqc/fastqc_2.cwl
  13     in:
  14       reads_file: fq
  15     out: [html_file]
  16
  17   STAR:
  18     requirements:
  19       ResourceRequirement:
  20         ramMin: 6000
  21     run: bio-cwl-tools/STAR/STAR-Align.cwl
  22     in:
  23       RunThreadN: {default: 4}
  24       GenomeDir: genome
  25       ForwardReads: fq
  26       OutSAMtype: {default: BAM}
  27       OutSAMunmapped: {default: Within}
  28     out: [alignment]
  29
  30   samtools:
  31     run: bio-cwl-tools/samtools/samtools_index.cwl
  32     in:
  33       bam_sorted: STAR/alignment
  34     out: [bam_sorted_indexed]
  35
  36   ### 8. Adding it to the workflow
  37   featureCounts:
  38     requirements:
  39       ResourceRequirement:
  40         ramMin: 500
  41     run: featureCounts.cwl
  42       in:
  43         counts_input_bam: samtools/bam_sorted_indexed
  44         gtf: gtf
  45       out: [featurecounts]
  46
  47 outputs:
  48   qc_html:
  49     type: File
  50     outputSource: fastqc/html_file
  51   bam_sorted_indexed:
  52     type: File
  53     outputSource: samtools/bam_sorted_indexed
  54
  55   ### 8. Adding it to the workflow
  56   featurecounts:
  57     type: File
  58       outputSource: featureCounts/featurecounts