multiple fastq for one sample

workflows/illumina_diversity_qc/__init__.py

@@ -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