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Update README.md
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Add update about snakemake version 8
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percyfal authored Apr 25, 2024
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Expand Up @@ -18,8 +18,6 @@ SnakemakeProfiles/slurm](https://github.com/Snakemake-Profiles/slurm/workflows/T
configuration](#parsing-arguments-to-slurm-sbatch-and-resource-configuration)
- [Rule specific resource
configuration](#rule-specific-resource-configuration)
- [Advanced argument conversion
(EXPERIMENTAL)](#advanced-argument-conversion-experimental)
- [Cluster configuration file](#cluster-configuration-file)
- [Tests](#tests)
- [Testing on a HPC running
Expand All @@ -30,11 +28,28 @@ SnakemakeProfiles/slurm](https://github.com/Snakemake-Profiles/slurm/workflows/T
- [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
Snakemake to run on the [SLURM Workload
Manager](https://slurm.schedmd.com/). The profile defines the following scripts
Manager](https://slurm.schedmd.com/) for **Snakemake version <=7**. The profile defines the following scripts

1. `slurm-submit.py` - submits a jobscript to slurm
2. `slurm-jobscript.sh` - a template jobscript
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