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fix: snakemake API using only 1 job as default #1283

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merged 2 commits into from Nov 29, 2021

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Maarten-vd-Sande
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@Maarten-vd-Sande Maarten-vd-Sande commented Nov 28, 2021

Description

The snakemake API specifies:

cores (int) – the number of provided cores (ignored when using cluster support) (default 1)
nodes (int) – the number of provided cluster nodes (ignored without cluster support) (default 1)

However 16c34c8 introduced a "bug" where if you use the api, e.g. snakemake.snakemake("Snakefile", cores=10) then cores would be set properly to 10, but nodes defaults to 1, so only one job at most works in parallel.

This should be fixed with this tiny change.

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).

edit

Ok somehow this gave an issue in the tests. The test needs 5 threads minimum due to many pipes, and only 3 were specified. That shouldn't have worked to begin with, so I would say this PR "works". However I'm not so sure why what I changed caused that bug to appear 🙃

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sonarcloud bot commented Nov 28, 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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@johanneskoester johanneskoester left a comment

Thanks a lot, LGTM!

@johanneskoester johanneskoester merged commit e92ad48 into snakemake:main Nov 29, 2021
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2 participants