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fix: unnecessary set Snakefile in AzBatch executor #2397

Merged
merged 4 commits into from Aug 7, 2023
Merged

fix: unnecessary set Snakefile in AzBatch executor #2397

merged 4 commits into from Aug 7, 2023

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jakevc
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@jakevc jakevc commented Aug 5, 2023 •
edited

Description

  • Removes unnecessary setting of Snakefile in AzBatch executor. This was 1. not necessary, and 2. was causing a failure to resolve the Snakefile path when it was located at workflow/Snakefile.
  • Since default resources is now included in the command per fix: do not overwrite default resources setting in azure batch executor #2395 , I needed to update the shell quoting so the command doesn't fail because of the parentheses in the default resources. Used the same solution as fix: slurm default_resources quoting #2043 and it works nicely.
  • Updated the masking regex to be more generic for SAS token possibilities

QC

  • 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).

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sonarcloud bot commented Aug 5, 2023

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 78e6d6e into main Aug 7, 2023
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@johanneskoester johanneskoester deleted the fix/azbatch branch August 7, 2023 08:28
@github-actions github-actions bot mentioned this pull request Aug 7, 2023
Merged
johanneskoester pushed a commit that referenced this pull request Aug 7, 2023
@github-actions
chore(main): release 7.32.2 (#2399)
1c5d154 
🤖 I have created a release *beep* *boop*
---


##
[7.32.2](v7.32.1...v7.32.2)
(2023-08-07)


### Bug Fixes

* unnecessary set Snakefile in AzBatch executor
([#2397](#2397))
([78e6d6e](78e6d6e))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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@johanneskoester johanneskoester johanneskoester approved these changes

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@jakevc @johanneskoester