lesson4/answers/part2/alignment.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   featureCounts:
  37     requirements:
  38       ResourceRequirement:
  39         ramMin: 500
  40     run: featureCounts.cwl
  41       in:
  42         counts_input_bam: samtools/bam_sorted_indexed
  43         gtf: gtf
  44       out: [featurecounts]
  45
  46 outputs:
  47   qc_html:
  48     type: File
  49     outputSource: fastqc/html_file
  50   bam_sorted_indexed:
  51     type: File
  52     outputSource: samtools/bam_sorted_indexed
  53
  54   featurecounts:
  55     type: File
  56       outputSource: featureCounts/featurecounts