Commit 04c4e197 authored by Claire Kuchly's avatar Claire Kuchly
Browse files

move to BWA mem

parent 39a0e8c0
......@@ -73,7 +73,7 @@ class IlluminaMatePair (CasavaNG6Workflow):
if self.group_prefix is not None :
sample_lane_prefixes = list((Utils.get_group_basenames(revcom1.output_files+revcom2.output_files, "lane")).keys())
#bwa = self.add_component("BWA", [indexed_ref, gunzip.fastq_R1 , gunzip.fastq_R2, sample_lane_prefixes], parent = cutadapt)
bwa = self.add_component("BWA", [indexed_ref, revcom1.output_files , revcom2.output_files, sample_lane_prefixes, 'aln', not self.delete_bam], parent = cutadapt)
bwa = self.add_component("BWA", [indexed_ref, revcom1.output_files , revcom2.output_files, sample_lane_prefixes, 'mem', not self.delete_bam], parent = cutadapt)
# make some statistic on the alignement
alignmentstats = self.add_component("AlignmentStats", [bwa.bam_files, self.is_paired_end(), False], parent = bwa)
......
......@@ -55,7 +55,7 @@ class IlluminaQualityCheck (CasavaNG6Workflow):
sample_lane_prefixes = None
if self.group_prefix != None :
sample_lane_prefixes = list((Utils.get_group_basenames(filtered_read1_files+filtered_read2_files, "lane")).keys())
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes, "aln", not self.delete_bam], parent = fastqilluminafilter)
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes, "mem", not self.delete_bam], parent = fastqilluminafilter)
# make some statistic on the alignement
alignmentstats = self.add_component("AlignmentStats", [bwa.bam_files, self.is_paired_end(), False], parent = bwa)
......
......@@ -52,7 +52,7 @@ class RnaSeqQualityCheck (CasavaNG6Workflow):
sample_lane_prefixes = None
if self.group_prefix != None :
sample_lane_prefixes = list((Utils.get_group_basenames(filtered_read1_files+filtered_read2_files, "lane")).keys())
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes, "aln", not self.delete_bam], parent = fastqilluminafilter)
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes, "mem", not self.delete_bam], parent = fastqilluminafilter)
# make some statistic on the alignement
alignmentstats = self.add_component("AlignmentStats", [bwa.bam_files, self.is_paired_end()], parent = bwa, component_prefix="bwa")
......@@ -90,4 +90,4 @@ class RnaSeqQualityCheck (CasavaNG6Workflow):
#Quality RNA Seq analysis
if self.annotation:
rseqc = self.add_component("RSeQC", [star.output_bams, self.annotation], parent = star)
\ No newline at end of file
rseqc = self.add_component("RSeQC", [star.output_bams, self.annotation], parent = star)
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