anchor.diff:        "module": "idseq_dag.steps.combine_json",
         "additional_files": {},
         "additional_attributes": {"field_idx": 4}
  +    },
  +    {
  +      "in": ["host_filter_out", "refined_gsnap_out", "refined_rapsearch2_out"],
  +      "out": "refined_annotated_out",
  +      "class": "PipelineStepGenerateAnnotatedFasta",
  +      "module": "idseq_dag.steps.generate_annotated_fasta",
  +      "additional_files": {},
  +      "additional_attributes": {}
  +    },
  +    {
  +      "in": ["refined_annotated_out", "refined_gsnap_out", "refined_rapsearch2_out"],
  +      "out": "refined_taxid_fasta_out",
  +      "class": "PipelineStepGenerateTaxidFasta",
  +      "module": "idseq_dag.steps.generate_taxid_fasta",
  +      "additional_files": {
  +        "lineage_db":  "<%= @attribute_dict[:lineage_db] %>"
  +      },
  +      "additional_attributes": {}
  +    },
  +    {
  +      "in": ["refined_taxid_fasta_out"],
  +      "out": "refined_taxid_locator_out",
  +      "class": "PipelineStepGenerateTaxidLocator",
  +      "module": "idseq_dag.steps.generate_taxid_locator",
  +      "additional_files": {},
  +      "additional_attributes": {}
       }
       <% end %>
     ],
  
positive.code:       "additional_attributes": {}
      },
      {
        "in": ["gsnap_m8", "taxid_locator_out"],
        "out": "alignment_viz_out",
        "class": "PipelineStepGenerateAlignmentViz",
        "module": "idseq_dag.steps.generate_alignment_viz",
  
negative.code:       "assembly/rapsearch2_contig_summary.json"
      ],
      "refined_taxon_count_out": ["assembly/refined_taxon_counts.json"],
      "contig_summary_out": ["assembly/combined_contig_summary.json"],
  
      "refined_annotated_out": ["assembly/refined_annotated_merged.fa", "assembly/refined_unidentified.fa"],
      "refined_taxid_fasta_out": ["assembly/refined_taxid_annot.fasta"],
      "refined_taxid_locator_out": [
        "assembly/refined_taxid_annot_sorted_nt.fasta",
        "assembly/refined_taxid_locations_nt.json",
        "assembly/refined_taxid_annot_sorted_nr.fasta",
        "assembly/refined_taxid_locations_nr.json",
        "assembly/refined_taxid_annot_sorted_genus_nt.fasta",
        "assembly/refined_taxid_locations_genus_nt.json",
        "assembly/refined_taxid_annot_sorted_genus_nr.fasta",
        "assembly/refined_taxid_locations_genus_nr.json",
        "assembly/refined_taxid_annot_sorted_family_nt.fasta",
        "assembly/refined_taxid_locations_family_nt.json",
        "assembly/refined_taxid_annot_sorted_family_nr.fasta",
        "assembly/refined_taxid_locations_family_nr.json",
        "assembly/refined_taxid_locations_combined.json"
      ]
      <% end %>
    },
    "steps": [
  