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fix: --conda-frontend value not passed on to cluster jobs #1317

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merged 2 commits into from Jan 11, 2022

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cjops
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@cjops cjops commented Jan 6, 2022

Description

Fixes #1108.

The --conda-frontend flag is now appended to the Snakemake command used by the ClusterExecutor and the CPUExecutor, just like --conda-prefix. The default of "mamba" no longer interferes if the user wishes to use "conda".

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).

@cjops cjops requested a review from johanneskoester as a code owner Jan 6, 2022
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sonarcloud bot commented Jan 11, 2022

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 df46ddb into snakemake:main Jan 11, 2022
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@jjs847
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jjs847 commented Feb 25, 2022

Hi, I am still having the issue of --conda-frontend value not being passed on to cluster jobs. I am using snakemake version 6.7.0

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--conda-frontend value not passed on to cluster jobs
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