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

feat: Add shadow: "copy-minimal" directive #1155

Merged
merged 4 commits into from Aug 27, 2021

Conversation

sebschmi
Copy link
Contributor

@sebschmi sebschmi commented Aug 26, 2021

"copy-minimal" is similar to "minimal", but it creates copies instead of symlinks of the files. This makes it possible to use local hard disks of a node in a cluster.

Description

See #1152 for motivation and further explanation.

I implemented the feature and added tests and documentation.
The test is a simple copy of the test_shadow test, removing all non-minimal parts and changing the minimal parts to copy-minimal, as well as testing if the files are physical copies instead of symlinks in the rules.
In the documentation I simply searched for "shadow" and added the description about the new feature at the necessary places.

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).

sebschmi added 2 commits Aug 26, 2021
"copy-minimal" is similar to "minimal", but it creates copies instead of symlinks of the files. This makes it possible to use local hard disks of a node in a cluster.

See snakemake#1152 for motivation and further explanation.

Closes snakemake#1152
@sebschmi sebschmi changed the title Implement and test shadow: "copy-minimal" directive. feat: Add shadow: "copy-minimal" directive Aug 26, 2021
@sonarcloud
Copy link

sonarcloud bot commented Aug 26, 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

@sebschmi sebschmi marked this pull request as ready for review Aug 26, 2021
@sebschmi sebschmi requested a review from johanneskoester as a code owner Aug 26, 2021
@johanneskoester
Copy link
Contributor

johanneskoester commented Aug 27, 2021

Good idea!

@johanneskoester johanneskoester merged commit 1803f0b into snakemake:main Aug 27, 2021
6 checks passed
@sebschmi sebschmi deleted the pull_request_1152 branch Aug 27, 2021
@DrYak
Copy link

DrYak commented Aug 29, 2021

Big thanks for this feature, I've dreamed for such a feature. That will so much help our use case! (currently I have a jury-rigged rsync-based solution ).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

3 participants