diff --git a/.gitignore b/.gitignore index 4c85108..79b599d 100644 --- a/.gitignore +++ b/.gitignore @@ -11,6 +11,9 @@ spec/reports test/tmp test/version_tmp tmp +*~ +*fastq +*config # YARD artifacts .yardoc diff --git a/bin/atron b/bin/atron index 62df4f2..bb2381a 100755 --- a/bin/atron +++ b/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 \ No newline at end of file diff --git a/lib/assemblotron.rb b/lib/assemblotron.rb index 2a9c6ce..c212712 100644 --- a/lib/assemblotron.rb +++ b/lib/assemblotron.rb @@ -39,4 +39,4 @@ module Assemblotron end Object.send :include, Yell::Loggable -end # Assemblotron +end # Assemblotron \ No newline at end of file diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.rb b/lib/assemblotron/assemblers/soap_denovo_trans.rb index 8eb1446..cf9aa10 100644 --- a/lib/assemblotron/assemblers/soap_denovo_trans.rb +++ b/lib/assemblotron/assemblers/soap_denovo_trans.rb @@ -129,4 +129,4 @@ def run_soap params end end -end # SoapDenovoTrans +end # SoapDenovoTrans \ No newline at end of file diff --git a/lib/assemblotron/assemblers/soap_denovo_trans.yml b/lib/assemblotron/assemblers/soap_denovo_trans.yml index a1fc2b5..01e6880 100644 --- a/lib/assemblotron/assemblers/soap_denovo_trans.yml +++ b/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 diff --git a/lib/assemblotron/objectives/no_score.rb b/lib/assemblotron/objectives/no_score.rb new file mode 100644 index 0000000..e6db862 --- /dev/null +++ b/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 diff --git a/test/test_soap_denovo_trans.rb b/test/test_soap_denovo_trans.rb index 290f882..3b6f80c 100644 --- a/test/test_soap_denovo_trans.rb +++ b/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,