def save_to_string(self, cmd: Command) -> str:
inputs: List[CliArgument] = [*cmd.named] + (
[] if self.ignore_positionals else [*cmd.positional])
names = self.choose_variable_names(inputs)
runtime = Task.Runtime()
runtime.add_docker(cmd.docker_image)
tool = Task(
name=self.make_task_name(cmd),
command=self.make_command(cmd, names),
version="1.0",
inputs=self.make_inputs(names),
outputs=self.make_outputs(names),
parameter_meta=self.make_parameter_meta(names),
runtime=runtime,
)
return tool.get_string()
def test_simple_task(self):
# Task based on: https://github.com/openwdl/wdl/blob/master/versions/draft-2/SPEC.md#introduction
t = Task("hello",
runtime=Task.Runtime(docker="broadinstitute/my_image"))
t.inputs.extend([
Input(WdlType.parse_type("String"), "pattern"),
Input(WdlType.parse_type("File"), "in"),
])
t.outputs.append(
Output(WdlType.parse_type("Array[String]"), "matches",
"read_lines(stdout())"))
t.command = Task.Command(
"egrep",
inputs=[Task.Command.CommandInput.from_input(i) for i in t.inputs])
print(t.get_string())
return t
