class CagnutPipelineDraw::Pipeline::Alignment
Attributes
bwa[RW]
picard[RW]
samtools[RW]
toolbox[RW]
Public Class Methods
new()
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 6 def initialize @config = Cagnut::Configuration.config @bwa = ::CagnutBwa::Util.new @config @samtools = ::CagnutSamtools::Util.new @picard = ::CagnutPicard::Util.new @config @toolbox = ::CagnutToolbox::Util.new @config end
Public Instance Methods
run(order=1)
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 14 def run order=1 case @config['data_type'] when 'BAM' puts 'Merging the following bam files' bam_dir = @config['bam_dir'] puts Dir.entries(bam_dir).select { |f| !File.directory? f } @samtools.merge_bam samtools_merge_bam_dirs, order when 'ONEFASTQ', 'ONEFASTQSE' job_name, order = @bwa.aln_one_fastq bwa_aln_dirs, order job_name, filename, order = @bwa.samp_one_fastq bwa_samp_dirs, order, job_name job_name, filename, order = @picard.add_or_replace_readgroups picard_add_read_group_dirs, order, job_name, filename @samtools.mg_bam_soft_link samtools_mg_bam_soft_link_dirs, order, job_name, filename else job_name, filename, order = @toolbox.qseq2fastq toolbox_qseq2fastq_dirs, order job_name, order = @bwa.aln bwa_aln_dirs, order, job_name, filename job_name, filename, order = @bwa.samp bwa_samp_dirs, order, job_name, filename job_name, filename, order = @picard.add_or_replace_readgroups picard_add_read_group_dirs, order, job_name, filename @samtools.merge_bam samtools_merge_bam_dirs, order, job_name, filename end end
Private Instance Methods
bwa_aln_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 50 def bwa_aln_dirs { output: @config['sample']['sai'] } end
bwa_samp_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 43 def bwa_samp_dirs { input: @config['sample']['sai'], output: @config['sample']['sam'] } end
picard_add_read_group_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 63 def picard_add_read_group_dirs { input: @config['sample']['sam'], output: @config['sample']['bam'], tmp_dir: @config['sample']['tmp'] } end
samtools_merge_bam_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 71 def samtools_merge_bam_dirs { input: @config['sample']['sam'], output: @config['sample']['bam'] } end
samtools_mg_bam_soft_link_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 56 def samtools_mg_bam_soft_link_dirs { input: @config['sample']['bam'], output: @config['sample']['bam'] } end
toolbox_qseq2fastq_dirs()
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# File lib/cagnut_pipeline_draw/pipeline/alignment.rb, line 37 def toolbox_qseq2fastq_dirs { output: @config['sample']['fastq'] } end