def _build_command(input_file, ref, novoalign_config): cmd = [ which("novoalign"), flatten_options(novoalign_config), "-o", "SAM", "-d", ref, "-f", input_file ] return list(map(str, flatten(cmd)))
def _build_command(input_file, tagdust_config, config): cl = [tagdust_config["program"], flatten_options(tagdust_config)] if "clean" in tagdust_config["keep"]: cl += ["-o", _build_output_file(input_file, "clean", config)] if "dirty" in tagdust_config["keep"]: cl += ["-a", _build_output_file(input_file, "dirty", config)] cl += [tagdust_config["contaminants"], input_file] return list(map(str, flatten(cl)))
def _build_command(input_file, ref, novoalign_config): cmd = [which("novoalign"), flatten_options(novoalign_config), "-o", "SAM", "-d", ref, "-f", input_file] return list(map(str, flatten(cmd)))