Python API

You can run a workflow from within Python by importing the snipgenie package and invoking the WorkFlow class. You need to provide the options in a dictionary with the same keywords as the command line. Notice in this example we are loading files from two folders.

import snipgenie
args = {'threads':8, 'outdir': 'results', 'labelsep':'-',
        'input':['/my/folder/',
                 '/my/other/folder'],
        'reference': 'sequence.fa', 'overwrite':False}
W = snipgenie.app.WorkFlow(**args)
W.setup()
W.run()