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percyfal authored Apr 25, 2024
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![Test
SnakemakeProfiles/slurm](https://github.com/Snakemake-Profiles/slurm/workflows/Test%20SnakemakeProfiles/slurm/badge.svg)

> [!IMPORTANT]
>
> ## Snakemake version 8 currently unsupported
>
> Snakemake version 8 introduces breaking changes with respect to the Snakemake cookiecutter profile. One new
> feature is that execution of jobs on a cluster or the cloud are handled by
> [executor plugins](https://snakemake.readthedocs.io/en/stable/tutorial/additional_features.html#cluster-or-cloud-execution).
> For instance, there is a
> [dedicated executor plugin for SLURM](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html) that
> provides much of the functionality that was previously catered for by this snakemake profile. Profiles are still needed, but their
> role changes somewhat to that of fine-tuning executor plugins for particular sites, only requiring the yaml configuration
> file.
>
> With this in mind, support for Snakemake version 8 has currently been put on hold and I recommend that users consult
> the executor plugin documentation for slurm.
>

# Contents

- [Introduction](#introduction)
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- [Anatomy of the tests (WIP)](#anatomy-of-the-tests-wip)
- [Adding new tests (WIP)](#adding-new-tests-wip)

> [!IMPORTANT]
>
> ## Snakemake version 8 unsupported
>
> Snakemake version 8 introduces breaking changes with respect to the Snakemake cookiecutter profile. One new
> feature is that execution of jobs on a cluster or the cloud are handled by
> [executor plugins](https://snakemake.readthedocs.io/en/stable/tutorial/additional_features.html#cluster-or-cloud-execution).
> For instance, there is a
> [dedicated executor plugin for SLURM](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html) that
> provides much of the functionality that was previously catered for by this snakemake profile. Profiles are still needed, but their
> role changes somewhat to that of fine-tuning executor plugins for particular sites, only requiring the yaml configuration
> file.
>
> With this in mind, support for Snakemake version 8 has currently been put on hold and I recommend that users consult
> the executor plugin documentation for slurm.
>
## Introduction

This cookiecutter provides a template Snakemake profile for configuring
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