def setup(self):
if not os.path.exists(self.args.out_dir):
os.mkdir(self.args.out_dir)
for fq in self.args.fastqs:
self.add_cmd(
PipelineCommandWrapper("Run FastQC", "fastqc", "-o",
self.args.out_dir, fq))
def test_piplinecommandwrapper(self):
# Make a pipeline command wrapper
cmd = PipelineCommandWrapper("Echo text", "echo", "hello")
# Check name and generated command
self.assertEqual(cmd.name(), "echo_text")
self.assertEqual(str(cmd.cmd()), "echo hello")
# Add argument and check updated command
cmd.add_args("there")
self.assertEqual(str(cmd.cmd()), "echo hello there")
def setup(self):
self.add_cmd(
PipelineCommandWrapper("Echo text to file", "echo",
self.args.s, ">>", self.args.f))
def setup(self):
self.fail(message="Invoked fail method", exit_code=123)
self.add_cmd(
PipelineCommandWrapper("Echo message", "echo",
"should not execute"))
def setup(self):
for i in xrange(self.args.n):
self.add_cmd(
PipelineCommandWrapper("Echo text", "echo",
self.args.s))
def setup(self):
self.add_cmd(
PipelineCommandWrapper("Nonexistant",
"./non_existant --help"))
