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kannon92mr-c
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feat: ran formatter
1 parent 77ba9ad commit 3ccf9ca

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3 files changed

+16
-7
lines changed

3 files changed

+16
-7
lines changed

cwltool/argparser.py

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -47,7 +47,6 @@ def arg_parser() -> argparse.ArgumentParser:
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help="Log your tools stdout/stderr to this location outside of container",
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)
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50-
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parser.add_argument(
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"--parallel",
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action="store_true",

cwltool/context.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -118,7 +118,7 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
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self.pull_image = True # type: bool
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self.rm_container = True # type: bool
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self.move_outputs = "move" # type: str
121-
self.log_dir = "" # type: str
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self.log_dir = "" # type: str
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self.streaming_allowed: bool = False
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self.singularity = False # type: bool

cwltool/job.py

Lines changed: 15 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -110,6 +110,7 @@ def relink_initialworkdir(
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def neverquote(string: str, pos: int = 0, endpos: int = 0) -> Optional[Match[str]]:
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return None
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CollectOutputsType = Union[Callable[[str, int], CWLObjectType], functools.partial]
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@@ -230,10 +231,15 @@ def is_streamable(file: str) -> bool:
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self.base_path_logs = self.outdir
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else:
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self.base_path_logs = runtimeContext.log_dir
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# Generate random ids
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# Generate random ids
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import uuid
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self.stdout = self.stdout if not self.stdout else self.stdout + uuid.uuid4().hex
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self.stderr = self.stderr if not self.stderr else self.stderr + uuid.uuid4().hex
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self.stdout = (
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self.stdout if not self.stdout else self.stdout + uuid.uuid4().hex
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)
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self.stderr = (
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self.stderr if not self.stderr else self.stderr + uuid.uuid4().hex
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)
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def _execute(
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self,
@@ -285,8 +291,12 @@ def _execute(
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]
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),
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" < %s" % self.stdin if self.stdin else "",
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" > %s" % os.path.join(self.base_path_logs, self.stdout) if self.stdout else "",
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" 2> %s" % os.path.join(self.base_path_logs, self.stderr) if self.stderr else "",
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" > %s" % os.path.join(self.base_path_logs, self.stdout)
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if self.stdout
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else "",
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" 2> %s" % os.path.join(self.base_path_logs, self.stderr)
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if self.stderr
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else "",
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)
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if self.joborder is not None and runtimeContext.research_obj is not None:
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job_order = self.joborder

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