fixes to loading config file and a few other little things

.gitignore

@@ -11,6 +11,9 @@ spec/reports
 test/tmp
 test/version_tmp
 tmp
+*~
+*fastq
+*config
 
 # YARD artifacts
 .yardoc

bin/atron

@@ -119,4 +119,4 @@ if !(options[:timelimit].nil?)
   options[:timelimit] = ChronicDuration.parse(options[:timelimit]);
 end
 
-Assemblotron::Controller.new(options).run
+Assemblotron::Controller.new(options).run

lib/assemblotron.rb

@@ -39,4 +39,4 @@ module Assemblotron
   end
   Object.send :include, Yell::Loggable
 
-end # Assemblotron
+end # Assemblotron

lib/assemblotron/assemblers/soap_denovo_trans.rb

@@ -129,4 +129,4 @@ def run_soap params
     end
   end
 
-end # SoapDenovoTrans
+end # SoapDenovoTrans

lib/assemblotron/assemblers/soap_denovo_trans.yml

@@ -3,11 +3,6 @@ name: SoapDenovoTrans
 shortname: sdt
 output: {}
 parameters:
-  config:
-    type: string
-    opt: false
-    desc: 'Path to SoapDenovoTrans config file'
-    required: true
   left:
     type: string
     opt: false

lib/assemblotron/objectives/no_score.rb

@@ -0,0 +1,12 @@
+# An objective function that returns 0
+#
+# This class conforms to the API for a Biopsy::ObjectiveFunction.
+class NoScore < Biopsy::ObjectiveFunction
+
+  # Don't do anything just return 0.
+  #
+  # @return [Integer] 0,
+  def run (raw_output, output_files, threads)
+    return 0
+  end
+end

test/test_soap_denovo_trans.rb

@@ -15,7 +15,7 @@ class TestSoapDenovoTrans < Minitest::Test
         :insertsize => '200',
         :l => 'l.fq',
         :r => 'r.fq',
-        :path => 'SOAPdenovo-Trans',
+        :path => 'SOAPdenovo-Trans-127mer',
         :memory => 12,
         :threads => 8,
         :out => 1,