def get(self, **wildcards):
missing = self.rule.wildcard_names.difference(wildcards.keys())
if missing:
raise WorkflowError("Missing wildcard values for {}".format(
", ".join(missing)))
output, _ = self.rule.expand_output(wildcards)
if (self.checkpoints.future_output is None or any(
(not f.exists or f in self.checkpoints.future_output)
for f in output)):
raise IncompleteCheckpointException(self.rule,
checkpoint_target(output[0]))
return CheckpointJob(self.rule, output)
def __init__(self, rule, targetfile):
super().__init__(
"The requested checkpoint output is not yet created."
"If you see this error, you have likely tried to use "
"checkpoint output outside of an input function, or "
"you have tried to call an input function directly "
"via <function_name>(). Please check the docs at "
"https://snakemake.readthedocs.io/en/stable/"
"snakefiles/rules.html#data-dependent-conditional-execution "
"and note that the input function in the example rule "
"'aggregate' is NOT called, but passed to the rule "
"by name, such that Snakemake can call it internally "
"once the checkpoint is finished.")
self.rule = rule
from snakemake.io import checkpoint_target
self.targetfile = checkpoint_target(targetfile)
def get(self, **wildcards):
missing = self.rule.wildcard_names.difference(wildcards.keys())
if missing:
raise WorkflowError("Missing wildcard values for {}".format(
", ".join(missing)))
output, _ = self.rule.expand_output(wildcards)
if self.checkpoints.future_output is not None:
for iofile in output:
if iofile in self.checkpoints.future_output:
break
if not iofile.exists and not iofile.is_temp:
break
else:
return CheckpointJob(self.rule, output)
raise IncompleteCheckpointException(self.rule,
checkpoint_target(output[0]))