class CagnutPipelineDraw::Pipeline::Recalibration
Attributes
gatk[RW]
picard[RW]
samtools[RW]
Public Class Methods
new(job_name)
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# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 6 def initialize job_name @job_name = job_name @config = Cagnut::Configuration.config @gatk = ::CagnutGatk::Util.new @config @picard = ::CagnutPicard::Util.new @config @samtools = ::CagnutSamtools::Util.new end
Public Instance Methods
run(filename = nil, order=1)
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# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 14 def run filename = nil, order=1 job_name, filename, order = picard.markdup picard_markup_dirs, order, @job_name, filename order = samtools.do_flag_stat samtools_do_flag_stat_dirs, order, job_name, filename order = gatk.count_read gatk_count_read_dirs, order, job_name, filename job_name, filename, order = gatk.recal gatk_recal_dirs, order, job_name, filename order = picard.picard_qc_metrics picard_picard_qc_metrics_dirs, order, job_name, filename [job_name, filename, order] end
Private Instance Methods
gatk_count_read_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 40 def gatk_count_read_dirs { input: @config['sample']['bam'], output: @config['sample']['stat'] } end
gatk_recal_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 47 def gatk_recal_dirs { input: @config['sample']['bam'], output: @config['sample']['bam'], contrast: @config['sample']['bam'] } end
picard_markup_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 25 def picard_markup_dirs { input: @config['sample']['bam'], output: @config['sample']['bam'], tmp_dir: @config['sample']['tmp'] } end
picard_picard_qc_metrics_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 55 def picard_picard_qc_metrics_dirs { input: @config['sample']['bam'], output: @config['sample']['stat'], tmp_dir: @config['sample']['tmp'] } end
samtools_do_flag_stat_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 33 def samtools_do_flag_stat_dirs { input: @config['sample']['bam'], output: @config['sample']['stat'] } end