self.add_parameter("barcode_file","Name of the barcode file",default=barcode_file,required=True,file_format='str')
#self.add_parameter("barcode_file", "Name of the barcode file", default=barcode_file, required=False , file_format = 'str')
self.add_parameter("archive_name","Name of the archive",default=archivename,type='str')
self.add_parameter("run_name","The name of the run (from total fastq file)",pattern='{basename_woext}',items=self.fastq_files,file_format="fastq")
#self.add_parameter( "run_name", "The name of the run (from total fastq file)", pattern='{basename_woext}', items=self.fastq_files, file_format = "fastq")
defdefine_analysis(self):
self.name="DemultiplexONT"
self.description="Demultiplexes the total fastq of a barcoded ONT run and produces stats"
self.software="Qcat"
#if self.discard_middle == "discard_middle":
# self.options = "--discard_middle"
self.description="Produces stats about demultiplex files from Qcat"