assets/answers/ep5/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: 9000
  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       SortedByCoordinate: {default: true}
  28       OutSAMunmapped: {default: Within}
  29     out: [alignment]
  30
  31   samtools:
  32     run: bio-cwl-tools/samtools/samtools_index.cwl
  33     in:
  34       bam_sorted: STAR/alignment
  35     out: [bam_sorted_indexed]
  36
  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   featurecounts:
  56     type: File
  57     outputSource: featureCounts/featurecounts