os.remove(x)
except:
pass
def complete(self):
exists = any([os.path.exists(x) for x in self.unglob])
return self.clone_parent().complete() and not exists
def output(self):
return self.input()
if __name__ == '__main__':
multiprocessing.set_start_method('forkserver')
logger, alloc_log = utils.logging_init(
log_dir=os.path.join(os.getcwd(), 'logs'),
pipeline_name=os.path.basename(__file__))
with open(sys.argv[1], 'r') as libs_file:
lib_list = [line.rstrip() for line in libs_file]
name = os.path.split(sys.argv[1])[1].split('.', 1)[0]
luigi.run([
'CleanUpCallset', '--output-prefix', name, '--lib-list',
json.dumps(lib_list), '--star-genome',
os.path.join(utils.reference_dir, 'genome'), '--reference',
os.path.join(utils.reference_dir, 'PST130_contigs.fasta'), '--mask',
os.path.join(utils.reference_dir, 'PST130_RNASeq_collapsed_exons.bed')
] + sys.argv[3:])
# This is a bit of a hack, it allows us to pass parameters to LibraryBatchWrapper and have them propagate
# down to all calls to PerLibPipeline.
library = None
def requires(self):
return [
self.clone_parent(library=lib.rstrip()) for lib in self.lib_list
]
def output(self):
return self.input()
# ----------------------------------------------------------------------- #
if __name__ == '__main__':
multiprocessing.set_start_method('forkserver')
logger, alloc_log = utils.logging_init(log_dir=os.path.join(
os.getcwd(), 'logs'),
pipeline_name=PIPELINE)
with open(sys.argv[1], 'r') as libs_file:
lib_list = [line.rstrip() for line in libs_file]
luigi.run([
'LibraryBatchWrapper', '--lib-list',
json.dumps(lib_list), '--star-genome',
os.path.join(utils.reference_dir, 'genome'), '--reference',
os.path.join(utils.reference_dir, 'PST130_contigs.fasta')
] + sys.argv[2:])