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, 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)))
