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Don't error on collision #5138

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merged 5 commits into from
Oct 31, 2024
Merged

Don't error on collision #5138

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7277316
Don't error on collision
stxue1 Oct 24, 2024
fec124c
Merge branch 'master' into issues/5137-collision-cwl-input-output
stxue1 Oct 24, 2024
02cc6de
Merge master into issues/5137-collision-cwl-input-output
github-actions[bot] Oct 25, 2024
a8c2a75
Merge master into issues/5137-collision-cwl-input-output
github-actions[bot] Oct 28, 2024
f6e1f75
Merge master into issues/5137-collision-cwl-input-output
github-actions[bot] Oct 30, 2024
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Don't error on collision
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@stxue1
stxue1 committed Oct 24, 2024
commit 72773164502f1cbe91185ad478b23d978055ae42
7 changes: 6 additions & 1 deletion src/toil/cwl/cwltoil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2366,7 +2366,12 @@ def _realpath(
# Probably staging and bypassing file store. Just copy.
logger.log(log_level, "Saving %s...", dest_url)
os.makedirs(os.path.dirname(p.target), exist_ok=True)
shutil.copyfile(p.resolved, p.target)
try:
shutil.copyfile(p.resolved, p.target)
except shutil.SameFileError:
# If outdir isn't set and we're passing through an input file/directory as the output,
# the file doesn't need to be copied because it is already there
pass
else:
uri = p.resolved
if not uri.startswith("toilfile:"):
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