#!/usr/bin/env cwl-runner
label: "Bacterial Annotation (two-pass)"
cwlVersion: v1.0
class: Workflow

requirements:
  - class: SubworkflowFeatureRequirement
  - class: MultipleInputFeatureRequirement

inputs:
  asn_cache: Directory
  inseq: File
  hmm_path: Directory
  hmms_tab: File
  uniColl_cache: Directory
  
  # Cached computational steps
  hmm_hits: File
  
outputs:
  aligns: 
    type: File
    outputSource: bacterial_hit_mapping/aligns
  # hmm_hits: 
  #   type: File
  #   outputSource: hmmsearch/hmm_hits
  # strace:
  #   type: File
  #   outputSource: hmmsearch/strace
    
  # proteins:
  #   type: File
  #   outputSource: protein_extract/proteins
  # lds2:
  #   type: File
  #   outputSource: protein_extract/lds2
  # seqids:
  #   type: File
  #   outputSource: protein_extract/seqids

steps:
  gp_getorf:
    run: gp_getorf.cwl
    in:
      asn_cache: asn_cache
      input: inseq
    out: [asncache, outseqs]

  protein_extract:
    run: protein_extract.cwl
    in:
      input: gp_getorf/outseqs
    out: [proteins, lds2, seqids]

  # Skipped due to compute cost, for now
  hmmsearch:
    run: wf_hmmsearch.cwl
    in:
      proteins: protein_extract/proteins
      hmm_path: hmm_path
      seqids: protein_extract/seqids
      lds2: protein_extract/lds2
      hmms_tab: hmms_tab
      asn_cache: gp_getorf/asncache
    out:
      [hmm_hits]
      #[strace]

  bacterial_hit_mapping:
    run: bacterial_hit_mapping.cwl
    in:
      seq_cache: gp_getorf/asncache
      unicoll_cache: uniColl_cache
      asn_cache: [gp_getorf/asncache, uniColl_cache]
      #hmm_hits: hmm_hits # Should be from hmmsearch
      hmm_hits: hmmsearch/hmm_hits
      sequences: gp_getorf/outseqs
    out: [asncache, aligns]

  get_off_frame_orfs:
    run: get_off_frame_orfs.cwl
    in:
      aligns: bacterial_hit_mapping/aligns
      seq_entries: gp_getorf/outseqs
    out: [prot_ids]