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fix: in rules from imported modules, exclude modified paths from module prefixing #1494

merged 11 commits into from Mar 23, 2022


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Initially, this only provides a test case for debugging. Here's the problem:

Currently, when importing a module (for example module imported_module:) with a path prefix: provided, that prefix also gets applied to paths that have been modified after loading the module with something like:

use rule x as imported_module_x with:
    input: "path/without/prefix/for/rewiring/input.txt"

As the example states, this precludes from properly rewiring the input of rules in that imported_module to output of rules from the importing / enclosing workflow or other imported modules.


  • 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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Please format your code with black: black snakemake tests/*.py.

@johanneskoester johanneskoester merged commit 1e73db0 into main Mar 23, 2022
@johanneskoester johanneskoester deleted the modules-test-no-prefixing-modified-paths branch March 23, 2022 12:12
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sonarcloud bot commented Mar 23, 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 1 Code Smell

No Coverage information No Coverage information
0.0% 0.0% Duplication

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2 participants