def variables():
v = ArgumentParser()
v.path = os.path.join(testpath, 'testdata', 'results')
v.targetpath = os.path.join(testpath, 'testdata', 'targets')
v.miseqpath = os.path.join(testpath, 'testdata')
v.miseqfolder = 'flowcell'
v.readlengthforward = '1'
v.readlengthreverse = '0'
v.customsamplesheet = os.path.join(v.miseqpath, v.miseqfolder,
'SampleSheet.csv')
v.copy = True
v.debug = True
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
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
