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)