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fix: Adds fixes for the first two MREs in #823 #1215

merged 7 commits into from Oct 25, 2021


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This PR extends @epruesse's fix in #1203. Importantly, it adds some changes to ensure that group jobs are marked finished, which fixes the second MRE in #823.

Together, the changes fix the first and second MREs in #823.


  • 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).

Maarten-vd-Sande and others added 4 commits September 22, 2021 12:12
- Incorporates @epruesse's fix for MRE snakemake#1
- Adds a fix for MRE snakemake#2 - properly marks group jobs as finished
- Some minor updates to tests
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@johanneskoester johanneskoester left a comment

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Thanks a lot!

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The tests seem to fail on windows for some reason. Can you have a look?

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sonarcloud bot commented Oct 23, 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

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Contributor Author

The second MRE was failing with due to the pipe() output.

I think the piped output is required for reproducing the behavior in #823, so it seems appropriate to skip the Windows test for now. It should be OK to remove the @skip_on_windows when pipe() is supported on Windows.

@johanneskoester johanneskoester merged commit cfd2f89 into snakemake:main Oct 25, 2021
@DonFreed DonFreed deleted the fix_checkpoint_finishing_823 branch October 26, 2021 04:27
pvandyken pushed a commit to pvandyken/snakemake that referenced this pull request Nov 15, 2021
* add failing tests 823

* fix mistakes

* black

* Fix the first two MREs from snakemake#823.

- Incorporates @epruesse's fix for MRE #1
- Adds a fix for MRE #2 - properly marks group jobs as finished
- Some minor updates to tests

* Fix tests on Windows

* Skip MRE 2 from 823 on Windows due to `pipe()` output

Co-authored-by: Maarten-vd-Sande <>
Co-authored-by: Johannes Köster <>
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3 participants