{
   "stages" : [
      {
         "name" : "call_features_rRNA_SEED"
      },
      {
         "name" : "call_features_tRNA_trnascan"
      },
      {
         "name" : "call_features_repeat_region_SEED",
         "repeat_region_SEED_parameters" : {
            "min_identity" : "95",
            "min_length" : "100"
         }
      },
      {
         "name" : "call_pyrrolysoproteins"
      },
      {
         "name" : "call_selenoproteins"
      },
      {
         "name" : "call_features_insertion_sequences"
      },
      {
         "name" : "call_features_strep_suis_repeat",
         "condition" : "$genome->{scientific_name} =~ /^Streptococcus\\s/"
      },
      {
         "name" : "call_features_strep_pneumo_repeat",
         "condition" : "$genome->{scientific_name} =~ /^Streptococcus\\s/"
      },
      {
         "name" : "call_features_crispr"
      },
      {
         "name" : "call_features_CDS_glimmer3",
         "glimmer3_parameters" : {
            "min_training_len" : "2000"
         }
      },
      {
         "name" : "call_features_CDS_prodigal"
      },
      {
         "name" : "annotate_proteins_kmer_v2",
         "kmer_v2_parameters" : {
            "min_hits" : "5"
         }
      },
      {
         "kmer_v1_parameters" : {
            "dataset_name" : "Release70",
            "annotate_hypothetical_only" : "1"
         },
         "name" : "annotate_proteins_kmer_v1"
      },
      {
         "name" : "annotate_proteins_similarity",
         "similarity_parameters" : {
            "annotate_hypothetical_only" : "1"
         }
      },
      {
         "name" : "resolve_overlapping_features",
         "resolve_overlapping_features_parameters" : {}
      },
      {
         "name" : "find_close_neighbors"
      },
      {
         "name" : "call_features_prophage_phispy"
      }
   ]
}