lesson1/answers/main.cwl

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