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Evaluate CWL jobs that should be skipped on the leader #5507

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Evaluate CWL jobs that should be skipped on the leader #5507

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20 changes: 14 additions & 6 deletions src/toil/cwl/cwltoil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2636,15 +2636,23 @@ def __init__(
# If not using the Toil file store, output files just go directly to
# their final homes their space doesn't need to be accounted per-job.

options_dict: dict = {} # type: ignore
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@annagiroti annagiroti May 15, 2026

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Is the # type: ignore here intentional? As far as I can tell dict = {} is valid Python and shouldn't produce a type error. Would dict[str, Any] be a more precise annotation, and would that remove the need for the ignore comment entirely?

run_local: bool = self.conditional.is_false(cwljob)
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@annagiroti annagiroti May 15, 2026

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cwljob may still have unresolved Promise objects at init time if when references an output from an upstream step. Since Conditional.is_false resolves promises without a file store, could this either crash or return the wrong result in that case? The worst case I can think of is is_false incorrectly returning True here, setting local=True with no resources, but then the fully-resolved condition at run() time returning False, meaning real work runs on the leader with no reserved resources. Would wrapping this in a try/except that falls back to run_local = False be a safe way to handle that?

if not run_local:
options_dict["cores"] = req["cores"]
options_dict["memory"] = memory
options_dict["disk"] = int(total_disk)
options_dict["accelerators"] = accelerators
options_dict["preemptible"] = preemptible

super().__init__(
cores=req["cores"],
memory=memory,
disk=int(total_disk),
accelerators=accelerators,
preemptible=preemptible,
tool_id=self.cwltool.tool["id"],
parent_name=parent_name,
local=isinstance(tool, cwltool.command_line_tool.ExpressionTool),
local=(
isinstance(tool, cwltool.command_line_tool.ExpressionTool)
or run_local
),
**options_dict,
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@annagiroti annagiroti May 15, 2026

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When run_local is True, options_dict is empty so cores, memory, disk, accelerators, and preemptible all fall back to Job defaults. CWLJobWrapper, which also runs locally, explicitly passes cores=1, memory="1GiB", disk="1MiB" for its local run. Would it be worth doing the same here for consistency, rather than relying on the defaults being equivalent?

)

self.cwljob = cwljob
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