assets/answers/ep3/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     # 4. Setting runtime RAM requirements
  19     requirements:
  20       ResourceRequirement:
  21         ramMin: 9000
  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       SortedByCoordinate: {default: true}
  29       OutSAMunmapped: {default: Within}
  30     out: [alignment]
  31
  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 outputs:
  39   qc_html:
  40     type: File
  41     outputSource: fastqc/html_file
  42   bam_sorted_indexed:
  43     type: File
  44     outputSource: samtools/bam_sorted_indexed