Commit 92a9f756 authored by Penom Nom's avatar Penom Nom
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parent ac81f78e
......@@ -77,9 +77,9 @@ class Methylseq (CasavaNG6Workflow):
if self.is_paired_end() and (self.group_prefix != None):
# split read 1 and read 2 from filtered files list
[concat_read1_files, concat_read2_files] = Utils.split_pair(concatenatefastq.concat_files, (self.group_prefix != None))
[concat_read1_files, concat_read2_files] = Utils.split_pair(concat_files, (self.group_prefix != None))
elif self.group_prefix != None:
concat_read1_files = concatenatefastq.concat_files
concat_read1_files = concat_files
concat_read2_files = []
else:
concat_read1_files = filtered_read1_files
......@@ -115,7 +115,7 @@ class Methylseq (CasavaNG6Workflow):
bismarkReference = self.add_component("Bismark", [indexed_ref,trim_galore.output_files_R1, None, self.samples_names, self.non_directional,self.bowtie2,self.alignment_mismatch,max_insert_size,"Library reads Alignment"],parent = trim_galore)
# compute the methylation extraction from the alignement
#bismarkReference_extract = self.add_component("BismarkMethylationExtractor", [indexed_ref, bismarkReference.output_bam, "single" , self.methylation_extractor_no_overlap], parent = bismarkReference)
'''
#Alignement against the control sequence if specified
if self.control_genome:
indexed_control = self.control_genome
......@@ -135,4 +135,4 @@ class Methylseq (CasavaNG6Workflow):
bismarkControl = self.add_component("Bismark", [indexed_control,trim_galore.output_files_R1, None ,self.samples_names, self.non_directional,self.bowtie2,self.alignment_mismatch,max_insert_size,"Control reads Alignment"], component_prefix="control", parent = trim_galore)
# compute the methylation extraction from the alignement
bismarkControl_extract = self.add_component("BismarkMethylationExtractor", [indexed_control, bismarkControl.output_bam, "single" , self.methylation_extractor_no_overlap], component_prefix="control", parent = bismarkControl)
'''
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