Commit 2e206f29 authored by Claire Kuchly's avatar Claire Kuchly
Browse files

multiple fastq for one sample

parent 725b1b00
......@@ -96,6 +96,9 @@ class IlluminaDiversityQC (NG6Workflow):
concatenatefastq = self.add_component("ConcatenateFilesGroups", [saved_files, reads_prefixes])
saved_files = concatenatefastq.concat_files
addrawfiles = self.add_component("AddRawFiles", [self.runobj, saved_files, self.args["compression"]])
concatenate1 = self.add_component("ConcatenateFilesGroups", [filtered_read1_files, (Utils.get_group_basenames(self.read1_files, "read")).keys()],component_prefix="read1")
concatenate2 = self.add_component("ConcatenateFilesGroups", [filtered_read2_files, (Utils.get_group_basenames(self.read2_files, "read")).keys()],component_prefix="read2")
# make some statistics on raw file
fastqc = self.add_component("FastQC", [filtered_read1_files+filtered_read2_files, (group_prefix is not None), True, run_name+"_fastqc.tar.gz"], parent = fastqilluminafilter)
......@@ -104,10 +107,10 @@ class IlluminaDiversityQC (NG6Workflow):
try: self.args["databank"].extend([self.get_resource("phix_bwa"), self.get_resource("ecoli_bwa"), self.get_resource("yeast_bwa")])
except: pass
if self.args["databank"]:
contamination_search = self.add_component("ContaminationSearch", [filtered_read1_files+filtered_read2_files, self.args["databank"], reads_prefixes], parent = fastqilluminafilter)
contamination_search = self.add_component("ContaminationSearch", [filtered_read1_files+filtered_read2_files, self.args["databank"], reads_prefixes], parent = fastqilluminafilter)
# merge overlapping pair
join_pairs = self.add_component("Flash", [filtered_read1_files, filtered_read2_files, self.args["mismatch_ratio"], self.args["min_overlap"], self.args["max_overlap"]], parent=fastqilluminafilter)
join_pairs = self.add_component("Flash", [concatenate1.concat_files, concatenate2.concat_files, self.args["mismatch_ratio"], self.args["min_overlap"], self.args["max_overlap"]], parent=fastqilluminafilter)
if self.args["assignation_databank"] is not None :
# subset assignation
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment