Add option to enable or disable trimming

workflows/ont_qc/__init__.py

@@ -30,6 +30,7 @@ class OntQualityCheck (NG6Workflow):
     def define_parameters(self, function="process"):
         logging.getLogger("jflow").debug("Begin OntQualityCheck.define_parameters! ont_qc")
         self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "gz")
+        self.add_parameter("trimming", "use trimming with porechop or not",choices= [ "yes", "no"], default = "yes")
         self.add_parameter("nb_threads", "Number of threads to use for porechop (default=16).", default=16)
         self.add_parameter("fileformat", "The file format for porechop (default=fastq).", choices= [ "fastq", "fasta"], default = "fastq")
         self.add_input_file( "summary_file", "Input summary basecalling file", default=None)
@@ -52,7 +53,8 @@ class OntQualityCheck (NG6Workflow):
         addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.get_all_reads(), self.compression])
         #nanoplot = self.add_component("Nanoplot", [sample.name,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
         ontstat = self.add_component("Run_stats", [self.summary_file, self.barcoded])
-        trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads(), self.nb_threads, self.fileformat , "discard_middle"])
+        if self.trimming == "yes":
+            trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads(), self.nb_threads, self.fileformat , "discard_middle"])
         if self.fast5dir != None:
             fast5archive = self.add_component("Fast5archive", [self.fast5dir, "fast5archive.tar"])