cwlVersion: v1.0
class: Workflow
id: kfdrc-annofuse-wf
requirements:
  - class: MultipleInputFeatureRequirement

inputs:
  sample_name: { type: 'string', doc: "Sample name to apply. Ought to be one from some kind of clinical database" }
  FusionGenome: { type: 'File', doc: "Tar ball with fusion_annot_lib.idx and blast_pairs.idx from STAR-Fusion CTAT Genome lib", "sbg:suggestedValue": { class: 'File', path: '63cff818facdd82011c8d6fe', name: 'GRCh38_v39_fusion_annot_custom.tar.gz' } }
  genome_untar_path: { type: 'string?', doc: "This is what the path will be when genome_tar is unpackaged", default: "GRCh38_v39_CTAT_lib_Mar242022.CUSTOM" }
  rsem_expr_file: { type: 'File', doc: "gzipped rsem gene expression file" }
  arriba_output_file: { type: 'File', doc: "Output from arriba, usually extension arriba.fusions.tsv" }
  col_num: { type: 'int?', doc: "0-based column number in file of fusion name, use 24 for arriba v1.1, 30 for v2", default: 30 }
  star_fusion_output_file: { type: 'File', doc: "Output from STAR Fusion, usually extension STAR.fusion_predictions.abridged.coding_effect.tsv" }
  output_basename: { type: 'string', doc: "String to use as basename for outputs" }

outputs:
  annofuse_filtered_fusions_tsv: { type: 'File?', outputSource: annoFuse_filter/filtered_fusions_tsv, doc: "Filtered output of formatted and annotated Star Fusion and arriba results" }

steps:
  format_arriba_output:
    run: ../tools/format_arriba_fusion_file.cwl
    in:
      arriba_fusion_file: arriba_output_file
      sample_name: sample_name
    out:
      [formatted_fusion_tsv]

  annotate_arriba:
    run: ../tools/fusion_annotator.cwl
    in:
      input_fusion_file: format_arriba_output/formatted_fusion_tsv
      genome_tar: FusionGenome
      genome_untar_path: genome_untar_path
      col_num: col_num
      output_basename: output_basename
    out:
      [annotated_tsv]

  annoFuse_filter:
    run: ../tools/annoFuse.cwl
    in:
      arriba_formatted_fusions: annotate_arriba/annotated_tsv
      starfusion_formatted_fusions: star_fusion_output_file
      rsem_expr_file: rsem_expr_file
      sample_name: sample_name
      output_basename: output_basename
    out:
      [filtered_fusions_tsv]

$namespaces:
  sbg: https://sevenbridges.com

hints:
  - class: 'sbg:AWSInstanceType'
    value: c5.2xlarge;ebs-gp2;400
    doc: "Chosen for speed and lower cost"