Commit 648e628e authored by maxime mano's avatar maxime mano
Browse files

Run with barcode visualisation, part 1 before migration to git

parent acb642e7
......@@ -29,9 +29,10 @@ 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 = "none")
self.add_parameter("nb_threads", "Number of threads to use for fastqc. Each thread will be allocated 250MB of memory.", default=6)
self.add_parameter("nanoplot_color", "Color of nanoplot")
#self.add_parameter("nb_threads", "Number of threads to use for fastqc. Each thread will be allocated 250MB of memory.", default=6)
#self.add_parameter("nanoplot_color", "Color of nanoplot")
self.add_input_file( "summary_file", "Input summary basecalling file", default=None)
self.add_parameter("barcoded", "", choices= [ "yes", "no"], default = "no")
def process(self):
logging.getLogger("jflow").debug("Begin OntQualityCheck.process! test ont_qc")
......@@ -48,5 +49,5 @@ class OntQualityCheck (NG6Workflow):
self.compression = "gz"
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])
ontstat = self.add_component("Run_stats", [self.summary_file, self.barcoded])
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