answers/ep2/main.cwl

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