nugen_barcode_splitter 0.0.2 → 0.0.3

data/bin/nugen_barcode_splitter

@@ -5,6 +5,7 @@ require "nugen_barcode_splitter"
 require "fileutils"
 
 usage =<<EOF
+      V E R S I O N - 0 . 0 . 3
       #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
 _____________________________________________________________________________
 

data/lib/nugen_barcode_splitter/nugen_template.rb

@@ -4,18 +4,17 @@ class NugenTemplate
 
   def initialize(fastq_multx, options)
     @template =<<EOF
-
-    #!/bin/bash
-    #\$ -pe DJ 4
-    #\$ -l h_vmem=6G
-    #\$ -j y
-    #\$ -N fq.Lane<%= @lane %>.<%= @number %>
-    #\$ -o <%= @lane_dir %>/nugen_demultiplexing.log
-
-    #{fastq_multx} #{options} -B <%= @barcodes %> \\
-      <(gunzip -c <%= @fwd %>) <(gunzip -c <%= @rev %>) \\
-      -o <%= @lane_dir %>/<%= @r1 %>.%.fq <%= @lane_dir %>/<%= @r2 %>.%.fq \\
-      >> <%= @lane_dir %>/nugen_demultiplexing.log
+#!/bin/bash
+#\$ -pe DJ 4
+#\$ -l h_vmem=6G
+#\$ -j y
+#\$ -N fq.Lane<%= @lane %>.<%= @number %>
+#\$ -o <%= @lane_dir %>/nugen_demultiplexing.log
+
+#{fastq_multx} #{options} -B <%= @barcodes %> \\
+  <(gunzip -c <%= @fwd %>) <(gunzip -c <%= @rev %>) \\
+  -o <%= @lane_dir %>/<%= @r1 %>.%.fq <%= @lane_dir %>/<%= @r2 %>.%.fq \\
+  >> <%= @lane_dir %>/nugen_demultiplexing.log
 EOF
   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.Lane_3.33\n    \#$ -o ~/Lane3//nugen_demultiplexing.log\n\n    fastq-multx  -B bc \\\n      fwd rev \\\n      -o R1_33.%.fq R2_33.%.fq\n")
+    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")
   end
 
   def test_fastq

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nugen_barcode_splitter
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
   prerelease: 
 platform: ruby
 authors: