nugen_barcode_splitter 0.0.8 → 0.0.9

data/bin/base_adder

@@ -15,7 +15,7 @@ file_dir = ARGV[0]
 number_of_bases = ARGV[1].to_i
 out_dir = ARGV[2]
 
-fastq = Fastq.new("file_dir")
+fastq = Fastq.new("#{file_dir}")
 fastq.add(number_of_bases, out_dir)
 fastq.close
 

data/bin/nugen_barcode_splitter

@@ -155,10 +155,10 @@ Dir.glob(options[:project_dir]+"/*").each do |p|
       STDERR.puts cmd if options[:debug]
     else
       status = system(cmd)
-      raise "Calling the template did not succeed!" if !status
+      raise "Calling base_adder did not succeed!" if !status
       cmd = "mv #{fwd}_added #{fwd}"
       status = system(cmd)
-      raise "Was not ablde to rename file #{fwd}!" if status!=true
+      raise "Was not able to rename file #{fwd}!" if status!=true
     end
   end
 

data/lib/nugen_barcode_splitter/sample_sheet.rb

@@ -30,6 +30,7 @@ class SampleSheet
       if current_lane != lane
         outfile = "#{prefix}_#{lane}.txt"
         current_lane = lane
+        handler.close()
         handler = File.new(outfile,'w')
         handler.write("# SampleName Barcode \n")
       end

data/test/test_mutations_caller_pipeline.rb

@@ -11,7 +11,7 @@ class NugenBarcodeSplitterTest < Test::Unit::TestCase
     assert template.to_s.include?("fastq-multx")
     assert template.to_s.include?("<%= @fwd %>")
     temp = template.fill("Lane_3", "33", "~/Lane3/", "bc", "fwd", "rev")
-    assert_equal(temp.to_s, "\n    #!/bin/bash\n    \#$ -pe DJ 4\n    \#$ -l h_vmem=6G\n    \#$ -j y\n    \#$ -N fq.LaneLane_3.33\n    \#$ -o ~/Lane3//nugen_demultiplexing.log\n\n    fastq-multx  -B bc \\\n      <(gunzip -c fwd) <(gunzip -c rev) \\\n      -o ~/Lane3//R1_33.%.fq ~/Lane3//R2_33.%.fq \\\n      >> ~/Lane3//nugen_demultiplexing.log\n")
+    assert_equal(temp.to_s, "fastq-multx  bc \\\n  <(gunzip -c fwd) \\\n  <(gunzip -c rev) \\\n  -o ~/Lane3//R1_33.%.fq ~/Lane3//R2_33.%.fq \\\n  >> ~/Lane3//nugen_demultiplexing.log\n")
   end
 
   def test_fastq

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nugen_barcode_splitter
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
   prerelease: 
 platform: ruby
 authors: