def decorate(ruleinfo):
if ruleinfo.wildcard_constraints:
rule.set_wildcard_constraints(
*ruleinfo.wildcard_constraints[0],
**ruleinfo.wildcard_constraints[1])
if ruleinfo.input:
rule.set_input(*ruleinfo.input[0], **ruleinfo.input[1])
if ruleinfo.output:
rule.set_output(*ruleinfo.output[0], **ruleinfo.output[1])
if ruleinfo.params:
rule.set_params(*ruleinfo.params[0], **ruleinfo.params[1])
# handle default resources
if self.default_resources is not None:
rule.resources = copy.deepcopy(self.default_resources.parsed)
if ruleinfo.threads is not None:
if (not isinstance(ruleinfo.threads, int)
and not isinstance(ruleinfo.threads, float)
and not callable(ruleinfo.threads)):
raise RuleException(
"Threads value has to be an integer, float, or a callable.",
rule=rule,
)
if name in self.overwrite_threads:
rule.resources["_cores"] = self.overwrite_threads[name]
else:
if isinstance(ruleinfo.threads, float):
ruleinfo.threads = int(ruleinfo.threads)
rule.resources["_cores"] = ruleinfo.threads
if ruleinfo.shadow_depth:
if ruleinfo.shadow_depth not in (True, "shallow", "full",
"minimal"):
raise RuleException(
"Shadow must either be 'minimal', 'shallow', 'full', "
"or True (equivalent to 'full')",
rule=rule,
)
if ruleinfo.shadow_depth is True:
rule.shadow_depth = "full"
logger.warning(
"Shadow is set to True in rule {} (equivalent to 'full'). It's encouraged to use the more explicit options 'minimal|shallow|full' instead."
.format(rule))
else:
rule.shadow_depth = ruleinfo.shadow_depth
if ruleinfo.resources:
args, resources = ruleinfo.resources
if args:
raise RuleException("Resources have to be named.")
if not all(
map(lambda r: isinstance(r, int) or callable(r),
resources.values())):
raise RuleException(
"Resources values have to be integers or callables",
rule=rule)
rule.resources.update(resources)
if ruleinfo.priority:
if not isinstance(ruleinfo.priority, int) and not isinstance(
ruleinfo.priority, float):
raise RuleException("Priority values have to be numeric.",
rule=rule)
rule.priority = ruleinfo.priority
if ruleinfo.version:
rule.version = ruleinfo.version
if ruleinfo.log:
rule.set_log(*ruleinfo.log[0], **ruleinfo.log[1])
if ruleinfo.message:
rule.message = ruleinfo.message
if ruleinfo.benchmark:
rule.benchmark = ruleinfo.benchmark
if not self.run_local and ruleinfo.group is not None:
rule.group = ruleinfo.group
if ruleinfo.wrapper:
rule.conda_env = snakemake.wrapper.get_conda_env(
ruleinfo.wrapper, prefix=self.wrapper_prefix)
# TODO retrieve suitable singularity image
if ruleinfo.env_modules:
# If using environment modules and they are defined for the rule,
# ignore conda and singularity directive below.
# The reason is that this is likely intended in order to use
# a software stack specifically compiled for a particular
# HPC cluster.
invalid_rule = not (ruleinfo.script or ruleinfo.wrapper
or ruleinfo.shellcmd or ruleinfo.notebook)
if invalid_rule:
raise RuleException(
"envmodules directive is only allowed with "
"shell, script, notebook, or wrapper directives (not with run)",
rule=rule,
)
from snakemake.deployment.env_modules import EnvModules
rule.env_modules = EnvModules(*ruleinfo.env_modules)
if ruleinfo.conda_env:
if not (ruleinfo.script or ruleinfo.wrapper
or ruleinfo.shellcmd or ruleinfo.notebook):
raise RuleException(
"Conda environments are only allowed "
"with shell, script, notebook, or wrapper directives "
"(not with run).",
rule=rule,
)
if not (urllib.parse.urlparse(ruleinfo.conda_env).scheme
or os.path.isabs(ruleinfo.conda_env)):
ruleinfo.conda_env = os.path.join(self.current_basedir,
ruleinfo.conda_env)
rule.conda_env = ruleinfo.conda_env
invalid_rule = not (ruleinfo.script or ruleinfo.wrapper
or ruleinfo.shellcmd or ruleinfo.notebook)
if ruleinfo.container_img:
if invalid_rule:
raise RuleException(
"Singularity directive is only allowed "
"with shell, script, notebook or wrapper directives "
"(not with run).",
rule=rule,
)
rule.container_img = ruleinfo.container_img
elif self.global_container_img:
if not invalid_rule:
# skip rules with run directive
rule.container_img = self.global_container_img
rule.norun = ruleinfo.norun
rule.docstring = ruleinfo.docstring
rule.run_func = ruleinfo.func
rule.shellcmd = ruleinfo.shellcmd
rule.script = ruleinfo.script
rule.notebook = ruleinfo.notebook
rule.wrapper = ruleinfo.wrapper
rule.cwl = ruleinfo.cwl
rule.restart_times = self.restart_times
rule.basedir = self.current_basedir
if ruleinfo.cache is True:
if not self.enable_cache:
logger.warning(
"Workflow defines that rule {} is eligible for caching between workflows "
"(use the --cache argument to enable this).".format(
rule.name))
else:
self.cache_rules.add(rule.name)
elif not (ruleinfo.cache is False):
raise WorkflowError(
"Invalid argument for 'cache:' directive. Only true allowed. "
"To deactivate caching, remove directive.",
rule=rule,
)
ruleinfo.func.__name__ = "__{}".format(rule.name)
self.globals[ruleinfo.func.__name__] = ruleinfo.func
setattr(rules, rule.name, RuleProxy(rule))
if checkpoint:
checkpoints.register(rule)
return ruleinfo.func
def decorate(ruleinfo):
if ruleinfo.wildcard_constraints:
rule.set_wildcard_constraints(
*ruleinfo.wildcard_constraints[0],
**ruleinfo.wildcard_constraints[1])
if ruleinfo.input:
rule.set_input(*ruleinfo.input[0], **ruleinfo.input[1])
if ruleinfo.output:
rule.set_output(*ruleinfo.output[0], **ruleinfo.output[1])
if ruleinfo.params:
rule.set_params(*ruleinfo.params[0], **ruleinfo.params[1])
# handle default resources
rule.resources = copy.deepcopy(self.default_resources)
if ruleinfo.threads:
if not isinstance(ruleinfo.threads, int) and not callable(
ruleinfo.threads):
raise RuleException(
"Threads value has to be an integer or a callable.",
rule=rule)
rule.resources["_cores"] = ruleinfo.threads
if ruleinfo.shadow_depth:
if ruleinfo.shadow_depth not in (True, "shallow", "full",
"minimal"):
raise RuleException(
"Shadow must either be 'minimal', 'shallow', 'full', "
"or True (equivalent to 'full')",
rule=rule)
if ruleinfo.shadow_depth is True:
rule.shadow_depth = 'full'
logger.warning(
"Shadow is set to True in rule {} (equivalent to 'full'). It's encouraged to use the more explicit options 'minimal|shallow|full' instead."
.format(rule))
else:
rule.shadow_depth = ruleinfo.shadow_depth
if ruleinfo.resources:
args, resources = ruleinfo.resources
if args:
raise RuleException("Resources have to be named.")
if not all(
map(lambda r: isinstance(r, int) or callable(r),
resources.values())):
raise RuleException(
"Resources values have to be integers or callables",
rule=rule)
rule.resources.update(resources)
if ruleinfo.priority:
if (not isinstance(ruleinfo.priority, int)
and not isinstance(ruleinfo.priority, float)):
raise RuleException("Priority values have to be numeric.",
rule=rule)
rule.priority = ruleinfo.priority
if ruleinfo.version:
rule.version = ruleinfo.version
if ruleinfo.log:
rule.set_log(*ruleinfo.log[0], **ruleinfo.log[1])
if ruleinfo.message:
rule.message = ruleinfo.message
if ruleinfo.benchmark:
rule.benchmark = ruleinfo.benchmark
if not self.run_local and ruleinfo.group is not None:
rule.group = ruleinfo.group
if ruleinfo.wrapper:
if self.use_conda:
rule.conda_env = snakemake.wrapper.get_conda_env(
ruleinfo.wrapper, prefix=self.wrapper_prefix)
# TODO retrieve suitable singularity image
if ruleinfo.conda_env and self.use_conda:
if not (ruleinfo.script or ruleinfo.wrapper
or ruleinfo.shellcmd):
raise RuleException(
"Conda environments are only allowed "
"with shell, script, or wrapper directives "
"(not with run).",
rule=rule)
if not (urllib.parse.urlparse(ruleinfo.conda_env).scheme
or os.path.isabs(ruleinfo.conda_env)):
ruleinfo.conda_env = os.path.join(self.current_basedir,
ruleinfo.conda_env)
rule.conda_env = ruleinfo.conda_env
if self.use_singularity:
invalid_rule = not (ruleinfo.script or ruleinfo.wrapper
or ruleinfo.shellcmd)
if ruleinfo.singularity_img:
if invalid_rule:
raise RuleException(
"Singularity directive is only allowed "
"with shell, script or wrapper directives "
"(not with run).",
rule=rule)
rule.singularity_img = ruleinfo.singularity_img
elif self.global_singularity_img:
if not invalid_rule:
# skip rules with run directive
rule.singularity_img = self.global_singularity_img
if self.use_docker:
#invalid_rule = not ruleinfo.shellcmd
invalid_rule = not (ruleinfo.script or ruleinfo.shellcmd)
if ruleinfo.docker_img:
if invalid_rule:
raise RuleException(
"docker_img directive is only allowed "
"with shell or script directives "
"(not with run/wrapper).",
rule=rule)
rule.docker_img = ruleinfo.docker_img
#elif self.global_singularity_img:
# if not invalid_rule:
# # skip rules with run directive
# rule.singularity_img = self.global_singularity_img
rule.norun = ruleinfo.norun
rule.docstring = ruleinfo.docstring
rule.run_func = ruleinfo.func
rule.shellcmd = ruleinfo.shellcmd
rule.script = ruleinfo.script
rule.wrapper = ruleinfo.wrapper
rule.cwl = ruleinfo.cwl
rule.restart_times = self.restart_times
rule.basedir = self.current_basedir
ruleinfo.func.__name__ = "__{}".format(rule.name)
self.globals[ruleinfo.func.__name__] = ruleinfo.func
setattr(rules, rule.name, RuleProxy(rule))
if checkpoint:
checkpoints.register(rule)
return ruleinfo.func