From 6f76ffe1d10c1c72aec806d729e2d866ca6fe80e Mon Sep 17 00:00:00 2001 From: Per Unneberg Date: Thu, 25 Apr 2024 15:13:17 +0200 Subject: [PATCH] Update README.md Add update about snakemake version 8 --- README.md | 21 ++++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 721dbb6..3fcfa26 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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