Commit a41a3010 authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

Add option to enable or disable trimming

parent 653760d4
......@@ -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"])
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