mutations_caller_pipeline_aws 0.0.6 → 0.0.7

data/bin/gatk_pipe_only_aws

@@ -44,7 +44,7 @@ options = { :bam_file_sorted => nil,
             :vcf => nil,
             :account => "",
             :project => "",
-            :debug = 1,
+            :debug => 1,
           }
 
 optparse = OptionParser.new do |opts|
@@ -113,7 +113,7 @@ options[:account] = options[:project] if options[:account].empty?
 # Indexing
 SamtoolsIndexing.call(bam_file,
                       job_prefix,
-                      account,
+                      options[:account],
                       options[:debug])
 
 # Realigne

data/lib/mutations_caller_pipeline_aws/bwa_caller.rb

@@ -10,7 +10,7 @@ class BwaCaller
   def self.call_paired_end(r1, r2, out_file, index, log_file, bwa, samtools, job_prefix,account, debug)
     cmd = "qsub -cwd -b y -N #{job_prefix}_bwa -l h_vmem=9G -pe make 4  #{account}\
       #{bwa} sampe -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
-        <(#{bwa} aln #{index} #{r1} 2>>#{log_file} || exit 1) <(#{bwa} aln #{index} #{r2} 2>>#{log_file} ) \
+        <(#{bwa} aln #{index} #{r1} 2>>#{log_file}) <(#{bwa} aln #{index} #{r2} 2>>#{log_file} ) \
         #{r1} #{r2} 2>>#{log_file} | #{samtools} view -Su - 2>>#{log_file} | #{samtools} sort - #{out_file} 2>>#{log_file}"
     puts cmd
     system('bash','-c', cmd) if debug == 1

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mutations_caller_pipeline_aws
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
   prerelease: 
 platform: ruby
 authors: