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added options for preparer

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khayer committed May 18, 2012
1 parent ff6a850 commit 5e9a931ce6b3eb502ee2d60e011ca38042a2cfb6
Showing with 24 additions and 2 deletions.
  1. +24 −2 bin/zebrafish_pipeline
  2. BIN zebrafish_pipeline-0.0.1.gem
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@@ -158,7 +158,9 @@ EOF
options = { :sam_file => nil,
:output_dir => "prepared.bam", :gatk => nil,
:bwa => nil, :account => "", :project => "",
- :debug => 1, :cluster => false,
+ :debug => 1, :cluster => false, :library => "zebrafish_lib",
+ :id => nil, :platform => "Illumina", :index => nil,
+ :sample_name => nil
}
options[:sam_file] = ARGV[1]
@@ -174,6 +176,14 @@ EOF
options[:output_dir] = i
end
+ opts.on("-m","--sample_name [name]", String,"Sample name") do |i|
+ options[:sample_name] = i if i
+ end
+
+ opts.on("-l","--library [name]", String,"Library used.") do |i|
+ options[:library] = i if i
+ end
+
opts.on("-s","--sge ", "Sun grid engine is available" ) do |i|
options[:sge] = true if i
end
@@ -194,6 +204,18 @@ EOF
options[:job_number] = i if i
end
+ opts.on("-i","--id [read group id]", String,"Read group ID must be different for each sample") do |i|
+ options[:id] = i if i
+ end
+
+ opts.on("-z","--platform [name]", String,"Platform. Default: Illumina") do |i|
+ options[:platform] = i if i
+ end
+
+ opts.on("-x","--index [name]", String,"Barcode index of Illumina run") do |i|
+ options[:index] = i if i
+ end
+
opts.on_tail("-h", "--help", "Show this message") do
puts opts
exit
@@ -202,7 +224,7 @@ EOF
begin
optparse.parse!
- mandatory = [:sam_file, :job_number, :bwa, :picard_tools, :gatk]
+ mandatory = [:sam_file, :job_number, :bwa, :picard_tools, :gatk, :id, :index, :sample_name]
missing = mandatory.select{ |param| options[param].nil? }
if !missing.empty?
puts "\n Missing options given or missing in config_file: \n\t#{missing.join(",\n\t")}"
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