#!/usr/bin/env cwl-runner
label: "PGAP Pipeline"
cwlVersion: v1.0
class: Workflow

requirements:
  - class: SubworkflowFeatureRequirement
  - class: MultipleInputFeatureRequirement
    
inputs:
  fasta: File
  submit_block_template: File
  taxid: int
  gc_assm_name: string

  # Cached computational steps
  hmm_hits: File
  
  # Auxillary files
  hmm_path: Directory
  hmms_tab: File
  uniColl_cache: Directory
  gene_master_ini: File
  16s_blastdb_dir: Directory
  23s_blastdb_dir: Directory
  model_path: File
  rfam_amendments: File
  rfam_stockholm: File

outputs:
  aligns: 
    type: File
    outputSource: bacterial_annot/aligns
  prok_entrez_gene_stuff: 
    type: File
    outputSource: cache_entrez_gene/prok_entrez_gene_stuff
  annotations_5s:
    type: File
    outputSource: bacterial_noncoding/annotations_5s
  annotations_16s:
    type: File
    outputSource: bacterial_noncoding/annotations_16s
  annotations_23s:
    type: File
    outputSource: bacterial_noncoding/annotations_23s
  
  # lds2: 
  #   type: File
  #   outputSource: bacterial_annot/lds2
  # seqids: 
  #   type: File
  #   outputSource: bacterial_annot/seqids
  #strace: 
  #  type: File
  #  outputSource: bacterial_annot/strace
  # sequences:
  #   type: File
  #   outputSource: bacterial_prepare_unannotated/sequences
  # asncache:
  #   type: Directory
  #   outputSource: bacterial_prepare_unannotated/asncache
    
steps:
  genomic_source:
    run: genomic_source/wf_genomic_source.cwl
    in:
      fasta: fasta
      submit_block_template: submit_block_template
      taxid: taxid
      gc_assm_name: gc_assm_name
    out: [gencoll_asn, seqid_list, stats_report, asncache]
    
  bacterial_prepare_unannotated:
    run: bacterial_prepare_unannotated.cwl
    in:
      asn_cache: genomic_source/asncache
      gc_assembly: genomic_source/gencoll_asn
      ids: genomic_source/seqid_list
      submit_block: submit_block_template
    out: [asncache, master_desc, sequences]

  cache_entrez_gene:
    run: cache_entrez_gene.cwl
    in:
      seq_cache: bacterial_prepare_unannotated/asncache
      unicoll_cache: uniColl_cache
      asn_cache: [bacterial_prepare_unannotated/asncache, uniColl_cache]
      egene_ini: gene_master_ini
      input: bacterial_prepare_unannotated/sequences
    out: [asncache, prok_entrez_gene_stuff]
      
      
  bacterial_annot:
    run: bacterial_annot/wf_bacterial_annot.cwl
    in:
      asn_cache: bacterial_prepare_unannotated/asncache
      inseq: bacterial_prepare_unannotated/sequences
      hmm_path: hmm_path
      hmms_tab: hmms_tab
      uniColl_cache: uniColl_cache
      hmm_hits: hmm_hits
    out:
      #[lds2,seqids]
      #[strace]
      #[hmm_hits]
      [aligns]

  bacterial_noncoding:
    run: bacterial_noncoding/wf_bacterial_noncoding.cwl
    in:
      asn_cache: genomic_source/asncache
      seqids: genomic_source/seqid_list
      16s_blastdb_dir: 16s_blastdb_dir
      23s_blastdb_dir: 23s_blastdb_dir
      model_path: model_path
      rfam_amendments: rfam_amendments
      rfam_stockholm: rfam_stockholm
    out: [ annotations_5s, annotations_16s, annotations_23s ]