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