anchor.diff:          <% end %>
         ],
       <% end %>
  -    "subsampled_out": [
  -      "subsampled_1.fa"
  -      <% if @attribute_dict[:fastq2] %>
  -        , "subsampled_2.fa", "subsampled_merged.fa"
  -      <% end %>
  -    ]
  -    ,
       "gsnap_filter_out": [
         "gsnap_filter_1.fa"
         <% if @attribute_dict[:fastq2] %>
  
positive.code:         , "bowtie2_2.fa", "bowtie2_merged.fa"
        <% end %>
      ],
      <% if @host_genome != "human" %>
        "star_human_out": [
          "unmapped_human_1.fa"
  
negative.code:       },
        "additional_attributes": { "output_sam_file": "bowtie2.sam" }
      }
      ,
      {
        "in": ["bowtie2_out"],
        "out": "subsampled_out",
        "class": "PipelineStepRunSubsample",
        "module": "idseq_dag.steps.run_subsample",
        "additional_files": {},
        "additional_attributes": { "max_fragments": <%= @attribute_dict[:max_subsample_frag] %> }
      },
      <% if @host_genome != "human" %>
      { 
        "in": ["subsampled_out", "validate_input_out"],
        "out": "star_human_out",
        "class": "PipelineStepRunStarDownstream",
        "module": "idseq_dag.steps.run_star_downstream",
        "additional_files": { "star_genome": "<%= @attribute_dict[:human_star_genome] %>" },
        "additional_attributes": {}
      },
      { 
        "in": ["star_human_out"],
        "out": "bowtie2_human_out",
        "class": "PipelineStepRunBowtie2",
        "module": "idseq_dag.steps.run_bowtie2",
        "additional_files": { "bowtie2_genome": "<%= @attribute_dict[:human_bowtie2_genome] %>" },
        "additional_attributes": { "output_sam_file": "bowtie2_human.sam" }
      },
      <% end %>
      {
        "in": [
          <% if @host_genome != "human" %>
            "bowtie2_human_out"
          <% else %>
            "subsampled_out"
          <% end %>
        ],
        "out": "gsnap_filter_out",
        "class": "PipelineStepRunGsnapFilter",
        "module": "idseq_dag.steps.run_gsnap_filter",
  