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
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
