Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix: issue #1257 (missing logfile failure when using shadow directory) #1258

merged 5 commits into from Nov 27, 2021


Copy link

@jaicher jaicher commented Nov 12, 2021


  • Test test_shadowed_log that demonstrates the failure case with issue Job failure with shadow directive if log files not created #1257
  • If logfile(s) were not created by job, Snakemake now creates empty logfile(s) in directory they would have been created in (i.e. shadow directory, if it was enabled) instead of its final destination. This allows snakemake.dag.unshadow_output(...) to successfully copy the logfile from the shadow directory to its final destination.


  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

This addresses gh snakemake#1257. If the rule did not create a logfile, an empty
one would be created in its final destination. If the shadow directive
was used, however, Snakemake would try to move the nonexistent logfile
from the shadow directory to its final location. This caused the
observed failures. This commit has Snakemake create the empty file where
Snakemake would have expected the program to create it (i.e. in the
shadow directory). This enables the unshadow operation that takes place
later to succeed.
@jaicher jaicher changed the title Fix missing logfile when using shadow directory (issue #1257) fix: issue #1257 (missing logfile failure when using shadow directory) Nov 12, 2021
Copy link

@johanneskoester johanneskoester left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks a lot, I have slightly modified your fix to also take care of remote files in the right way.

Copy link

sonarcloud bot commented Nov 26, 2021

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@johanneskoester johanneskoester merged commit 426d92f into snakemake:main Nov 27, 2021
@jaicher jaicher deleted the fix-missing-shadowed-logs branch December 1, 2021 20:46
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
None yet
None yet

Successfully merging this pull request may close these issues.

None yet

2 participants