Commit 0fc44600 authored by maxime mano's avatar maxime mano
Browse files

Add the Runstats analysis for the ONT data

parent 1c51484c
......@@ -29,12 +29,8 @@ 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=3)
#self.add_parameter("min_subreads_length", "Subreads shorter than this value (in base pairs) are filtered out and excluded from analysis", default=0, type='int')
#self.add_parameter("polymerase_read_qual", "Polymerase reads with lower quality than this value are filtered out and excluded from analysis", default=0, type='float')
#self.add_parameter("polymerase_read_length", "Polymerase reads shorter than this value (in base pairs) are filtered out and excluded from analysis", default=0, type='int')
#self.add_parameter("barcode_score", "Min identical base for barcode", default=22, type='int')
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)
def process(self):
......@@ -45,10 +41,12 @@ class OntQualityCheck (NG6Workflow):
sample_names.append( sample.name )
infiles.append(sample.reads1[0])
# add raw
print(self.get_all_reads())
print(sample_names)
print(self.summary_file)
self.compression = "gz"
addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.get_all_reads(), self.compression])
#add_ont_raw_file = self.add_component("AddOntRawFiles", [self.runobj, self.get_all_reads()])
#h5tofastq = self.add_component("H5toFastq", [sample_names, infiles])
#fastqc = self.add_component("FastQC", [h5tofastq.output_fastqs, False, False, "fastqc.tar.gz", self.nb_threads], parent = h5tofastq)
#self.add_component("RS_Subreads", [sample_names, infiles,self.min_subreads_length,self.polymerase_read_qual,self.polymerase_read_length,self.barcode_file,self.barcode_score ])
#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])
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