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When a rule given in a ``ruleorder`` statement is missing, the exception (raised in https://github.com/snakemake/snakemake/blob/74db8e59f584c3ddbb7acb974e57865f4b819d04/snakemake/workflow.py#L553) cur…
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Hi, is it possible that the snakemake implementation supports single "tumour-only" samples? It looks as though it doesn't, or at least this usage is not described. I am making a snakemake workflow em…
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## Purpose
To get consensus on what the Vulcan config should look like.
Context:
Typically a snakemake pipeline is just:
- a Snakefile
- a config
- some scripts.
A vulcan pipeline …
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**Snakemake version**
8.14.0
**Describe the bug**
When a Snakemake module imports its Python module, a `ModuleNotFoundError` is raised. However, when the module is executed on its own, no such er…
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[coverage_table.zip](https://github.com/user-attachments/files/16685684/coverage_table.zip)
Dr. Francisco Zorrilla
Hello!
When using metaGEM for analysis, I encountered an issue involving fea…
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I tried to run
https://github.com/PyPSA/pypsa-eur/blob/master/scripts/prepare_sector_network.py
as python script to debug and learn about it.
I got an error due to non-existing config file
…
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**Snakemake version**
8.4.7
**Describe the bug**
On Windows write_source_archive in workflow.py tries to write to C://Tempfile//Path/snakemake-sources.tar.xz rather than C:/Tempfile/Path/snakemak…
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Currently my machine has conda with just the conda-forge channel, meaning the instructions in https://github.com/pyani-plus/pyani-plus/blob/main/CONTRIBUTING.md failed when trying to install snakemake…
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Don't know how easy this is to do with an extension, but an annoyance of writing workflows in VS Code is the implicitly defined `snakemake` global variable. The type checker is not aware of this and w…
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At the moment the workflow waits for each experiment to finish before submitting another. Would be nice to be able to submit one after another without waiting.