mutations_caller_pipeline_aws 0.0.16 → 0.0.17

data/bin/mutations_caller_pipeline_aws

@@ -30,7 +30,7 @@ ________________________________________________________________________________
   Also you should have the indices for bwa and GATK prepared.
   NOTE: Only paired end reads are supported!
 
-                      +++  C L U S T E R  V E R S I O N - 0.0.15 +++
+                      +++  C L U S T E R  V E R S I O N - 0.0.17 +++
 
   config.yml should look like this:
   # config.yml
@@ -157,8 +157,8 @@ def run(options)
   job_number = options[:job_number]
   bam_file = "aligned_#{job_number}.bam"
   bam_file_sorted = "sorted_#{job_number}.bam"
-  bam_file_sorted_dublicates = options[:step_one_bam_file]
-  dublicate_metrcis = "GATK_files/dublicate.metrics"
+  bam_file_sorted_duplicates = options[:step_one_bam_file]
+  duplicate_metrcis = "GATK_files/duplicates.metrics"
   job_prefix = "#{job_number}"
   log_file = "log/#{options[:sample_name]}.log"
 
@@ -181,8 +181,8 @@ def run(options)
     puts cmd
   end
 
-  cmd = PicardCaller.mark_dublicates(bam_file_sorted, bam_file_sorted_dublicates,
-    dublicate_metrcis, options[:picard_tools], log_file, job_prefix,
+  cmd = PicardCaller.mark_duplicates(bam_file_sorted, bam_file_sorted_duplicates,
+    duplicate_metrcis, options[:picard_tools], log_file, job_prefix,
     options[:account])
 
   if options[:debug] == 1
@@ -191,7 +191,7 @@ def run(options)
     puts cmd
   end
 
-  cmd = PicardCaller.build_index(bam_file_sorted_dublicates,
+  cmd = PicardCaller.build_index(bam_file_sorted_duplicates,
     options[:picard_tools], log_file, job_prefix, options[:account])
 
   if options[:debug] == 1

data/lib/mutations_caller_pipeline_aws/picard_caller.rb

@@ -13,16 +13,16 @@ class PicardCaller
   end
 
 
-  #mark_dublicates = "java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/MarkDuplicates.jar I=WT_aligned_sorted_rg.bam O=marked_dublicates.bam M=dublicate.metrcis AS=true VALIDATION_STRINGENCY=LENIENT"
-  def self.mark_dublicates(bam_file_sorted, bam_file_sorted_dublicates, duplicate_metrcis, picard_tools, log_file, job_prefix, account)
+  #mark_duplicates = "java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/MarkDuplicates.jar I=WT_aligned_sorted_rg.bam O=marked_dublicates.bam M=dublicate.metrcis AS=true VALIDATION_STRINGENCY=LENIENT"
+  def self.mark_duplicates(bam_file_sorted, bam_file_sorted_duplicates, duplicate_metrcis, picard_tools, log_file, job_prefix, account)
     cmd = "qsub -o #{log_file} -e #{log_file}_duplicates_errors -V -cwd -b y -hold_jid sort_#{job_prefix} -N duplicates_#{job_prefix} -l h_vmem=7G #{account} \
-      java -Xmx3g -jar #{picard_tools}/MarkDuplicates.jar I=#{bam_file_sorted} O=#{bam_file_sorted_dublicates} M=#{duplicate_metrcis} \
+      java -Xmx3g -jar #{picard_tools}/MarkDuplicates.jar I=#{bam_file_sorted} O=#{bam_file_sorted_duplicates} M=#{duplicate_metrcis} \
       AS=true VALIDATION_STRINGENCY=LENIENT"
   end
 
   #build_index = "java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/BuildBamIndex.jar I=marked_dublicates.bam  VALIDATION_STRINGENCY=LENIENT"
-  def self.build_index(bam_file_sorted_dublicates, picard_tools, log_file, job_prefix, account)
-    cmd = "qsub -o #{log_file} -e #{log_file}_index_errors -V -cwd -b y -hold_jid dublicates_#{job_prefix} -N index_#{job_prefix} -l h_vmem=7G #{account} \
-      java -Xmx3g -jar #{picard_tools}/BuildBamIndex.jar I=#{bam_file_sorted_dublicates}  VALIDATION_STRINGENCY=LENIENT"
+  def self.build_index(bam_file_sorted_duplicates, picard_tools, log_file, job_prefix, account)
+    cmd = "qsub -o #{log_file} -e #{log_file}_index_errors -V -cwd -b y -hold_jid duplicates_#{job_prefix} -N index_#{job_prefix} -l h_vmem=7G #{account} \
+      java -Xmx3g -jar #{picard_tools}/BuildBamIndex.jar I=#{bam_file_sorted_duplicates}  VALIDATION_STRINGENCY=LENIENT"
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mutations_caller_pipeline_aws
 version: !ruby/object:Gem::Version
-  version: 0.0.16
+  version: 0.0.17
   prerelease: 
 platform: ruby
 authors: