def _run(args, base_dir, workflows_dir, config_path):
"""
Run a complete workflow.
"""
if not os.path.exists(config_path):
sys.stdout.write(
f"The config file: {config_path} does not exist.\nProvide a path to the config file with "
f"--config or if you do not have a config file run:\n"
f"seq2science init {args.workflow}\n")
sys.exit(1)
# parse the args
parsed_args = {
"snakefile":
os.path.join(workflows_dir, args.workflow.replace("-", "_"),
"Snakefile"),
"use_conda":
True,
"conda_frontend":
conda_frontend,
"conda_prefix":
os.path.join(base_dir, ".snakemake"),
"dryrun":
args.dryrun,
"printreason":
args.reason,
"keepgoing":
args.keep_going,
"unlock":
args.unlock,
"force_incomplete":
args.rerun_incomplete
}
# get the additional snakemake options
snakemake_options = args.snakemakeOptions if args.snakemakeOptions is not None else dict(
)
snakemake_options.setdefault("config", {}).update(
{"rule_dir": os.path.join(base_dir, "rules")})
# parse the profile
snakemake_options["configfiles"] = [config_path]
if args.profile is not None:
profile_file = snakemake.get_profile_file(args.profile, "config.yaml")
if profile_file is None:
print("Error: profile given but no config.yaml found.")
sys.exit(1)
snakemake_options["configfiles"] += [profile_file]
parsed_args.update(snakemake_options)
# cores
if args.cores: # CLI
parsed_args["cores"] = args.cores
elif parsed_args.get("cores"): # profile
parsed_args["cores"] = int(parsed_args["cores"])
elif parsed_args["dryrun"]:
parsed_args["cores"] = 999
else:
parsed_args["cores"] = 0
if parsed_args["cores"] < 2:
# we need to raise an exception and catch it for a subjectively prettier message
try:
raise argparse.ArgumentError(core_arg,
"specify at least two cores.")
except argparse.ArgumentError as e:
print() # empty line
print(e)
sys.exit(1)
core_parser(parsed_args)
# run snakemake
exit_code = snakemake.snakemake(**parsed_args)
sys.exit(0) if exit_code else sys.exit(1)
def _explain(args, base_dir, workflows_dir, config_path):
"""
Run a complete dryrun workflow, then return the explanations of each rule used.
"""
if not os.path.exists(config_path):
sys.stdout.write(
f"The config file: {config_path} does not exist.\nProvide a path to the config file with "
f"--config or if you do not have a config file run:\n"
f"seq2science init {args.workflow}\n")
sys.exit(1)
# parse the args
parsed_args = {
"snakefile":
os.path.join(workflows_dir, args.workflow.replace("-", "_"),
"Snakefile"),
"dryrun":
True,
"forceall":
True,
"quiet":
False
}
# get the additional snakemake options
snakemake_options = args.snakemakeOptions if args.snakemakeOptions is not None else dict(
)
snakemake_options.setdefault("config", {}).update(
{"rule_dir": os.path.join(base_dir, "rules")})
# parse the profile
snakemake_options["configfiles"] = [config_path]
if args.profile is not None:
profile_file = snakemake.get_profile_file(args.profile, "config.yaml")
if profile_file is None:
print("Error: profile given but no config.yaml found.")
sys.exit(1)
snakemake_options["configfiles"] += [profile_file]
parsed_args.update(snakemake_options)
# cores
parsed_args["cores"] = 999
# starting message
rules_used = {
"start":
f"\nPreprocessing of reads was done automatically with workflow tool "
f"seq2science v{seq2science.__version__} (https://doi.org/10.5281/zenodo.3921913)."
}
def log_handler(log):
if log["level"] == "job_info" and "msg" in log and log[
"msg"] is not None and log["name"] not in rules_used:
rules_used[log["name"]] = log["msg"]
parsed_args["log_handler"] = [log_handler]
parsed_args["config"]["explain_rule"] = True
# run snakemake (silently)
with open(os.devnull, "w") as null:
with contextlib.redirect_stdout(null), contextlib.redirect_stderr(
null):
exit_code = snakemake.snakemake(**parsed_args)
print(" ".join(rules_used.values()))
sys.exit(0) if exit_code else sys.exit(1)
def _run(args, base_dir, workflows_dir, config_path):
"""
Run a complete workflow.
"""
if not os.path.exists(config_path):
sys.stdout.write(
f"The config file: {config_path} does not exist.\nProvide a path to the config file with "
f"--config or if you do not have a config file run:\n"
f"seq2science init {args.workflow}\n")
sys.exit(1)
# parse the args
parsed_args = {
"snakefile":
os.path.join(workflows_dir, args.workflow.replace("-", "_"),
"Snakefile"),
"use_conda":
True,
"conda_frontend":
conda_frontend,
"conda_prefix":
os.path.join(base_dir, ".snakemake"),
"dryrun":
args.dryrun,
"printreason":
args.reason,
"keepgoing":
args.keep_going,
"unlock":
args.unlock,
"force_incomplete":
args.rerun_incomplete
}
# get the additional snakemake options
snakemake_options = args.snakemakeOptions if args.snakemakeOptions is not None else dict(
)
snakemake_options.setdefault("config", {}).update(
{"rule_dir": os.path.join(base_dir, "rules")})
snakemake_options["configfiles"] = [config_path]
parsed_args.update(snakemake_options)
# parse the profile
if args.profile is not None:
profile_file = snakemake.get_profile_file(args.profile, "config.yaml")
if profile_file is None:
subjectively_prettier_error(
profile_arg, "profile given but no config.yaml found.")
add_profile_args(profile_file, parsed_args)
# cores
if args.cores: # CLI
parsed_args["cores"] = args.cores
elif parsed_args.get("cores"): # profile
parsed_args["cores"] = int(parsed_args["cores"])
elif parsed_args["dryrun"]:
parsed_args["cores"] = 999
else:
parsed_args["cores"] = 0
if parsed_args["cores"] < 2:
subjectively_prettier_error(core_arg, "specify at least two cores.")
# when running on a cluster assume cores == nodes (just like snakemake does)
if "cluster" in parsed_args and not "nodes" in parsed_args:
parsed_args["nodes"] = parsed_args["cores"]
core_parser(parsed_args)
parsed_args["config"].update({"cores": parsed_args["cores"]})
resource_parser(parsed_args)
# run snakemake
exit_code = snakemake.snakemake(**parsed_args)
sys.exit(0) if exit_code else sys.exit(1)