class CagnutPipelineDraw::Pipeline::VariantCall
Attributes
gatk[RW]
snp_eff[RW]
Public Class Methods
new(job_name)
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# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 6 def initialize job_name @job_name = job_name @config = Cagnut::Configuration.config @gatk = ::CagnutGatk::Util.new @config @snpeff = ::CagnutSnpeff::Util.new end
Public Instance Methods
run(filename = nil, order=1)
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# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 13 def run filename = nil, order=1 order = @gatk.depth_of_coverage gatk_depth_of_coverage_dirs, order, @job_name, filename job_name, filename, order = @gatk.unified_genotyper gatk_unified_genotyper_dirs, order, @job_name, filename job_name, filename, order = @gatk.snpcal gatk_snpcal_dirs, order, job_name, filename job_name, order = @snpeff.snp_annotation snpeff_snp_annotation_dirs, order, job_name, filename # collectSPeekMetrics [job_name, nil, order+1] end
Private Instance Methods
gatk_depth_of_coverage_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 24 def gatk_depth_of_coverage_dirs { input: @config['sample']['bam'], output: @config['sample']['stat'], } end
gatk_snpcal_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 31 def gatk_snpcal_dirs { input: @config['sample']['bam'], output: @config['sample']['vcf'], } end
gatk_unified_genotyper_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 38 def gatk_unified_genotyper_dirs { input: @config['sample']['vcf'], output: @config['sample']['vcf'], } end
snpeff_snp_annotation_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 45 def snpeff_snp_annotation_dirs { input: @config['sample']['vcf'], output: @config['sample']['vcf'], } end