<commit_before>cwlVersion: v1.0
class: Workflow

requirements:
  - class: InlineJavascriptRequirement
  - class: StepInputExpressionRequirement

inputs:
  jobid : int
  api_key: string?
  db_dir: Directory
  no-shock:
    type: boolean?
    default: true
  sequences: File
  rna:
    type: boolean?
    default: true
  rna_nr_clust: File  
  rna_nr: File
  rna_nr_version: string
  rna_pid: int
  rna_assembled: boolean
  rna_clust_memory:
    type: int
    default: 20
    
      

outputs:
  rnaFile:
    type: File
    outputSource: searchRNA/rna
  clusterFile:
    type: File
    outputSource: clusterRNA/fasta  
  sims: 
    type: File
    outputSource: simsRNA/sims
 
  
        
steps:
  searchRNA:
    run: ../Tools/awe_search_rna.tool.yaml
    in:
      input: sequences
      output: 
        source: jobid
        valueFrom: $(self).425.search.rna.fna
      rna_nr: rna_nr_clust
      no-shock: no-shock
       
    out: [rna]

  clusterRNA:
    run: ../Tools/awe_cluster.tool.yaml
    in:
      input: searchRNA/rna 
      out_prefix: 
        source: jobid
        valueFrom: $(self).440.cluster
      pid: rna_pid
      memory: rna_clust_memory
      no-shock: no-shock  
      exclusive_parameters: 
        source: rna<commit_msg>Added missing mapping file option<commit_after>cwlVersion: v1.0
class: Workflow

requirements:
  - class: InlineJavascriptRequirement
  - class: StepInputExpressionRequirement

inputs:
  jobid : int
  api_key: string?
  db_dir: Directory
  no-shock:
    type: boolean?
    default: true
  sequences: File
  rna:
    type: boolean?
    default: true
  rna_nr_clust: File  
  rna_nr: File
  rna_nr_version: string
  rna_pid: int
  rna_assembled: boolean
  rna_clust_memory:
    type: int
    default: 20
    
      

outputs:
  rnaFile:
    type: File
    outputSource: searchRNA/rna
  clusterFile:
    type: File
    outputSource: clusterRNA/fasta  
  mapping:
    type: File
    outputSource: clusterRNA/mapping  
  sims: 
    type: File
    outputSource: simsRNA/sims
 
  
        
steps:
  searchRNA:
    run: ../Tools/awe_search_rna.tool.yaml
    in:
      input: sequences
      output: 
        source: jobid
        valueFrom: $(self).425.search.rna.fna
      rna_nr: rna_nr_clust
      no-shock: no-shock
       
    out: [rna]

  clusterRNA:
    run: ../Tools/awe_cluster.tool.yaml
    in:
      input: searchRNA/rna 
      out_prefix: 
        source: jobid
        valueFrom: $(self).440.cluster
      pid: rna_pid
      memory: rna_clust_memory
      no-shock: no-shock  
      exclusive_parameters: 
        source: rna
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