mutations_caller_pipeline_aws 0.0.6 → 0.0.7
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data/bin/gatk_pipe_only_aws
CHANGED
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@@ -44,7 +44,7 @@ options = { :bam_file_sorted => nil,
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44
44
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:vcf => nil,
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45
45
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:account => "",
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46
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:project => "",
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47
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-
:debug
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47
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+
:debug => 1,
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}
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optparse = OptionParser.new do |opts|
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@@ -113,7 +113,7 @@ options[:account] = options[:project] if options[:account].empty?
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113
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# Indexing
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SamtoolsIndexing.call(bam_file,
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job_prefix,
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116
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-
account,
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116
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+
options[:account],
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options[:debug])
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# Realigne
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@@ -10,7 +10,7 @@ class BwaCaller
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def self.call_paired_end(r1, r2, out_file, index, log_file, bwa, samtools, job_prefix,account, debug)
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cmd = "qsub -cwd -b y -N #{job_prefix}_bwa -l h_vmem=9G -pe make 4 #{account}\
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#{bwa} sampe -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
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-
<(#{bwa} aln #{index} #{r1} 2>>#{log_file}
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+
<(#{bwa} aln #{index} #{r1} 2>>#{log_file}) <(#{bwa} aln #{index} #{r2} 2>>#{log_file} ) \
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#{r1} #{r2} 2>>#{log_file} | #{samtools} view -Su - 2>>#{log_file} | #{samtools} sort - #{out_file} 2>>#{log_file}"
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puts cmd
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system('bash','-c', cmd) if debug == 1
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