anchor.diff:      <% if @attribute_dict[:fastq2] %>
         "fastqs": ["<%= @attribute_dict[:fastq1] %>", "<%= @attribute_dict[:fastq2] %>"],
         "star_out": ["unmapped1.<%= @attribute_dict[:file_type] %>", "unmapped2.<%= @attribute_dict[:file_type] %>"],
  -      <% if @dag_vars_dict["trimmomatic"] %>
  -        "trimmomatic_out": ["trimmomatic1.<%= @attribute_dict[:file_type] %>", "trimmomatic2.<%= @attribute_dict[:file_type] %>"],
  -      <% end %>
  +      "trimmomatic_out": ["trimmomatic1.<%= @attribute_dict[:file_type] %>", "trimmomatic2.<%= @attribute_dict[:file_type] %>"],
         "priceseq_out": ["priceseq1.fa", "priceseq2.fa"],
         "cdhitdup_out": ["dedup1.fa", "dedup2.fa"],
         "lzw_out": ["lzw1.fa", "lzw2.fa"],
  
positive.code:     <% else %>
        "fastqs": ["<%= @attribute_dict[:fastq1] %>"],
        "star_out": ["unmapped1.<%= @attribute_dict[:file_type] %>"],
        <% if @dag_vars_dict["trimmomatic"] %>
          "trimmomatic_out": ["trimmomatic1.<%= @attribute_dict[:file_type] %>"],
        <% end %>
        "priceseq_out": ["priceseq1.fa"],
        "cdhitdup_out": ["dedup1.fa"],
        "lzw_out": ["lzw1.fa"],
  
negative.code:       "additional_attributes": { "truncate_fragments_to": <%= @attribute_dict[:max_fragments] %>
                                  ,"output_gene_file": "reads_per_gene.star.tab" }
      },
      {
        "in": ["star_out"],
        "out": "trimmomatic_out",
        "class": "PipelineStepRunTrimmomatic",
        "module": "idseq_dag.steps.run_trimmomatic",
        "additional_files": {
          "adapter_fasta": "<%= @attribute_dict[:adapter_fasta] %>"
        },
        "additional_attributes": {}
      },
      {
        "in": [
            "trimmomatic_out"
        ],
        "out": "priceseq_out",
        "class": "PipelineStepRunPriceSeq",
  