mutations_caller_pipeline_aws 0.0.9 → 0.0.10

data/lib/mutations_caller_pipeline_aws/bwa_caller.rb

@@ -8,7 +8,7 @@ class BwaCaller
   end
 
   def self.call_paired_end(r1, r2, out_file, index, log_file, bwa, samtools, job_prefix,account, debug)
-    cmd = "qsub -cwd -b y -N bwa_#{job_prefix} -l h_vmem=9G -pe make 4  #{account}\
+    cmd = "qsub -V -cwd -b y -N bwa_#{job_prefix} -l h_vmem=9G -pe make 4  #{account}\
       #{bwa} sampe -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
         <(#{bwa} aln #{index} #{r1} 2>>#{log_file}) <(#{bwa} aln #{index} #{r2} 2>>#{log_file} ) \
         #{r1} #{r2} 2>>#{log_file} | #{samtools} view -Su - 2>>#{log_file} | #{samtools} sort - #{out_file} 2>>#{log_file}"

data/lib/mutations_caller_pipeline_aws/gatk_caller.rb

@@ -3,7 +3,7 @@ class GatkCaller
   # Genotyper
   def self.call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account, debug)
     cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
-      qsub -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=3G -hold_jid recalibration_#{job_prefix} #{account}\
+      qsub -V -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=3G -hold_jid recalibration_#{job_prefix} #{account}\
       #{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \
       -I #{read_bam} \
       -o #{read_vcf} \
@@ -16,7 +16,7 @@ class GatkCaller
   # Making recalibration table
   def self.recalibrate_bam(log_dir ,gatk, index_fa, index_vcf, read_bam, recal_file, job_prefix, account, debug )
     cmd = "echo 'starting recalibration table ' `date` >> #{log_dir}
-      qsub -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=4G  -hold_jid realignment_#{job_prefix} #{account} \
+      qsub -V -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=4G  -hold_jid realignment_#{job_prefix} #{account} \
       #{gatk} -knownSites #{index_vcf} -I #{read_bam} \
       -R #{index_fa} -T CountCovariates \
       -cov ReadGroupCovariate -cov QualityScoreCovariate -cov DinucCovariate \
@@ -29,7 +29,7 @@ class GatkCaller
   # Using recalibration table
   def self.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file, job_prefix, account, debug)
     cmd = "echo 'recalibrating bam_file at ' `date` >> #{log_dir}
-      qsub -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=4G -hold_jid recalibration_table_#{job_prefix} #{account} \
+      qsub -V -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=4G -hold_jid recalibration_table_#{job_prefix} #{account} \
       #{gatk} \
       -R #{index_fa} \
       -I #{read_bam} \
@@ -43,7 +43,7 @@ class GatkCaller
   # Preparation realignement
   def self.prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals, job_prefix, account, debug)
     cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
-      qsub -cwd -b y -N prep_realignment_#{job_prefix} -l h_vmem=4G -hold_jid indexing_#{job_prefix} #{account}\
+      qsub -V -cwd -b y -N prep_realignment_#{job_prefix} -l h_vmem=4G -hold_jid indexing_#{job_prefix} #{account}\
       #{gatk} \
       -I #{read_bam} \
       -R #{index_fa} \
@@ -56,7 +56,7 @@ class GatkCaller
   # Realignment
   def self.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam, job_prefix, account, debug)
     cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
-      qsub -cwd -b y -N realignment_#{job_prefix} -l h_vmem=4G -hold_jid prep_realignment_#{job_prefix} #{account} \
+      qsub -V -cwd -b y -N realignment_#{job_prefix} -l h_vmem=4G -hold_jid prep_realignment_#{job_prefix} #{account} \
       #{gatk} \
       -I #{read_bam} \
       -R #{index_fa} \

data/lib/mutations_caller_pipeline_aws/samtools_indexing.rb

@@ -1,6 +1,6 @@
 class SamtoolsIndexing
   def self.call(bam_file, job_prefix, account, debug)
-    cmd = "qsub -cwd -b y -N indexing_#{job_prefix} -l h_vmem=3G -hold_jid bwa_#{job_prefix} #{account} \
+    cmd = "qsub -V -cwd -b y -N indexing_#{job_prefix} -l h_vmem=3G -hold_jid bwa_#{job_prefix} #{account} \
       samtools index #{bam_file}"
     puts cmd
     system(cmd) if debug == 1

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mutations_caller_pipeline_aws
 version: !ruby/object:Gem::Version
-  version: 0.0.9
+  version: 0.0.10
   prerelease: 
 platform: ruby
 authors: