anchor.diff:        "additional_attributes": {}
       },
       {
  -      "in": ["gsnap_m8", "taxid_locator_out"],
  +      "in": [
  +        "gsnap_m8", 
  +        "taxid_locator_out"
  +        <% if @dag_vars_dict["assembly"] %>
  +          ,"gsnap_accessions_out"
  +        <% end %>
  +      ],
         "out": "alignment_viz_out",
         "class": "PipelineStepGenerateAlignmentViz",
         "module": "idseq_dag.steps.generate_alignment_viz",
  
positive.code:       "assembly/rapsearch2_contig_summary.json"
      ],
      "refined_taxon_count_out": ["assembly/refined_taxon_counts.json"],
      "contig_summary_out": ["assembly/combined_contig_summary.json"]
  
      <% end %>
    },
    "steps": [
  
negative.code:       "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 %>
    ],
  