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

[dlaehnemann]

Description

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.

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).

[github-actions]

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

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

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1 Code Smell

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