testing = False
experiment_name = '10percent-test'
description = 'A larger test set to test out the data on'
# Preprocessing
#===============================================================================
W = Workflow()
W.create_new(name='zebras-gazelles-test', testing=testing)
# Make sure barcodes and datafiles are in their right folders
if testing:
W.add_datafiles(data_files='testset_500.fastq.bgzf' , barcode_files='*[8].txt')
else:
W.add_datafiles(data_files='lane6*bgzf' , barcode_files='*[6].txt')
W.add_datafiles(data_files='lane8*bgzf' , barcode_files='*[8].txt')
# Set parameters
p = {'filtering' : {'propN': 0.1,
'phred': 25,
'cutsite_edit_dist' : 2,
'overhang_edit_dist' : 0},
'cleaning' : {'max_edit_dist' : 1 }}
if testing:
W.setup_preprocessing(infiles_pattern="testset_500.fastq.bgzf" , params=p)
else:
W.setup_preprocessing(infiles_pattern="lane*.bgzf" , params=p)
experiment_name = ""
description = ""
dataset_name = ""
testing = False
# Preprocessing
# ===============================================================================
W = Workflow()
W.create_new(name=dataset_name, testing=testing)
# Make sure barcodes and datafiles are in their right folders
if testing:
W.add_datafiles(data_files="testset_500.fastq.bgzf", barcode_files="*[8].txt")
else:
W.add_datafiles(data_files="*.bgzf", barcode_files="*.txt")
W.add_datafiles(data_files="*.bgzf", barcode_files="*.txt")
# Set parameters
p = {
"filtering": {"propN": 0.1, "phred": 25, "cutsite_edit_dist": 2, "overhang_edit_dist": 0},
"cleaning": {"max_edit_dist": 1},
}
if testing:
W.setup_preprocessing(infiles_pattern="testset_500.fastq.bgzf", params=p)
else:
W.setup_preprocessing(infiles_pattern="*.bgzf", params=p)
