def create_args(): arguments = ArgumentParser() arguments.sequencepath = test_sequences_path arguments.starttime = time() arguments.reportpath = os.path.join(arguments.sequencepath, 'reports') arguments.runmetadata = MetadataObject() # Create metadata objects for the samples arguments.runmetadata.samples = Filer.filer(arguments) return arguments
def variables(): v = ArgumentParser() v.sequencepath = os.path.join(testpath, 'testdata') v.referencefilepath = os.path.join(v.sequencepath, 'databases') v.customsamplesheet = os.path.join(v.sequencepath, 'SampleSheet.csv') v.debug = True v.numreads = 2 v.kmerrange = '21' v.preprocess = False v.basicassembly = True v.threads = multiprocessing.cpu_count() v.startingtime = time() v.commit = b'' v.homepath = scriptpath return v