RNA-Seq/cwl/helper/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 requirements:
  11   StepInputExpressionRequirement: {}
  12
  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   STAR:
  21     requirements:
  22       ResourceRequirement:
  23         ramMin: 9000
  24     run: bio-cwl-tools/STAR/STAR-Align.cwl
  25     in:
  26       RunThreadN: {default: 4}
  27       GenomeDir: genome
  28       ForwardReads: fq
  29       OutSAMtype: {default: BAM}
  30       SortedByCoordinate: {default: true}
  31       OutSAMunmapped: {default: Within}
  32       ### 1. Expressions on step inputs
  33       OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
  34     out: [alignment]
  35
  36   samtools:
  37     run: bio-cwl-tools/samtools/samtools_index.cwl
  38     in:
  39       bam_sorted: STAR/alignment
  40     out: [bam_sorted_indexed]
  41
  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