mutations_caller_pipeline_aws 0.0.16 → 0.0.17
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@@ -30,7 +30,7 @@ ________________________________________________________________________________
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Also you should have the indices for bwa and GATK prepared.
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NOTE: Only paired end reads are supported!
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-
+++ C L U S T E R V E R S I O N - 0.0.
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+
+++ C L U S T E R V E R S I O N - 0.0.17 +++
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config.yml should look like this:
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# config.yml
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@@ -157,8 +157,8 @@ def run(options)
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job_number = options[:job_number]
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bam_file = "aligned_#{job_number}.bam"
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bam_file_sorted = "sorted_#{job_number}.bam"
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-
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-
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+
bam_file_sorted_duplicates = options[:step_one_bam_file]
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duplicate_metrcis = "GATK_files/duplicates.metrics"
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job_prefix = "#{job_number}"
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log_file = "log/#{options[:sample_name]}.log"
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@@ -181,8 +181,8 @@ def run(options)
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puts cmd
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end
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-
cmd = PicardCaller.
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-
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+
cmd = PicardCaller.mark_duplicates(bam_file_sorted, bam_file_sorted_duplicates,
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duplicate_metrcis, options[:picard_tools], log_file, job_prefix,
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options[:account])
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if options[:debug] == 1
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@@ -191,7 +191,7 @@ def run(options)
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puts cmd
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end
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-
cmd = PicardCaller.build_index(
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+
cmd = PicardCaller.build_index(bam_file_sorted_duplicates,
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options[:picard_tools], log_file, job_prefix, options[:account])
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if options[:debug] == 1
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@@ -13,16 +13,16 @@ class PicardCaller
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end
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-
#
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def self.
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#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"
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def self.mark_duplicates(bam_file_sorted, bam_file_sorted_duplicates, duplicate_metrcis, picard_tools, log_file, job_prefix, account)
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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} \
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-
java -Xmx3g -jar #{picard_tools}/MarkDuplicates.jar I=#{bam_file_sorted} O=#{
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java -Xmx3g -jar #{picard_tools}/MarkDuplicates.jar I=#{bam_file_sorted} O=#{bam_file_sorted_duplicates} M=#{duplicate_metrcis} \
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AS=true VALIDATION_STRINGENCY=LENIENT"
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end
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#build_index = "java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/BuildBamIndex.jar I=marked_dublicates.bam VALIDATION_STRINGENCY=LENIENT"
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-
def self.build_index(
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-
cmd = "qsub -o #{log_file} -e #{log_file}_index_errors -V -cwd -b y -hold_jid
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-
java -Xmx3g -jar #{picard_tools}/BuildBamIndex.jar I=#{
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def self.build_index(bam_file_sorted_duplicates, picard_tools, log_file, job_prefix, account)
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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} \
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java -Xmx3g -jar #{picard_tools}/BuildBamIndex.jar I=#{bam_file_sorted_duplicates} VALIDATION_STRINGENCY=LENIENT"
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end
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end
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