mutations_caller_pipeline_aws 0.0.13 → 0.0.14

data/bin/mutations_caller_pipeline_aws

@@ -92,11 +92,11 @@ optparse = OptionParser.new do |opts|
   end
 
   opts.on("-p","--cluster ", "On compute cluster (none AWS)" ) do |i|
-    options[:cluster] =  true
+    options[:cluster] =  true if i
   end
 
   opts.on("-o","--coverage ", "GATK Coverage summary" ) do |i|
-    options[:coverage] =  true
+    options[:coverage] =  true if i
   end
 
   opts.on_tail("-h", "--help", "Show this message") do
@@ -240,6 +240,7 @@ if options[:coverage]
     options[:gatk],
     options[:index_fa],
     recal_bam,
+    outfile_prefix,
     job_prefix,
     options[:account],
     options[:debug])

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: mutations_caller_pipeline_aws
 version: !ruby/object:Gem::Version 
-  hash: 5
+  hash: 3
   prerelease: 
   segments: 
   - 0
   - 0
-  - 13
-  version: 0.0.13
+  - 14
+  version: 0.0.14
 platform: ruby
 authors: 
 - Kaharina Hayer