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: snakemake API using only 1 job as default #1283

merged 2 commits into from Nov 29, 2021


Copy link

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


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.


  • 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).


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 🙃

Copy link

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

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, LGTM!

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