illumina_quality_kraken2:
    label: Kraken2
    doc: Taxonomic classification of FASTQ reads
    when: $(inputs.kraken_database !== null)
    in:
      tmp_id: identifier
      identifier:
        valueFrom: $(inputs.tmp_id)_Qfiltered
      threads: threads
      kraken_database: kraken_database
      database: kraken_database
      forward_reads: phix_filter/out_forward_reads
      reverse_reads: phix_filter/out_reverse_reads
      paired_end: 
        default: true
    run: 
      class: Worflow
      inputs:
        identifier: string  # a guess at the type
        threads: int  # a guess at the type
        kraken_database: File[]  # replace with the real type
        forward_reads: Any  # replace with the real type
        reverse_reads: Any  # replace with the real type
        paired_end: bool
      steps:
        kraken2:
          run: ../kraken2/kraken2.cwl
          scatter: database
          in:
            identifier: identifier
            threads: threads
            kraken_database: kraken_database
            database: kraken_database
            forward_reads: forward_reads
            reverse_reads: reverse_reads
            paired_end: paired_end 
          out: [sample_report]
      outputs:
        sample_report:
          type: File[]  # replace with the real type
    out: [sample_report]