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+---
+created_at: 2025-11-10
+title: snakemake
+tags: []
+---
+
+[//]:snakemake.md> (APPS PAGE BOILERPLATE START)
+{% set app_name = page.title | trim %}
+{% set app = applications[app_name] %}
+{% include "partials/app_header.html" %}
+[//]:snakemake.md> (APPS PAGE BOILERPLATE END)
+
+## Snakemake job groups
+
+Please use [Snakemake's job grouping](https://snakemake.readthedocs.io/en/stable/executing/grouping.html) functionality to avoid Snakemake submitting many short jobs to the queue. Each job submitted to Slurm should take at least 30 minutes.
+
+## Running Snakemake in an interactive Slurm session
+
+Request an interactive Slurm session with the resources required to run all subjobs labeled as `localrules`:
+
+```
+srun --account nesi12345
+```
+
+Once the interactive session has launched, load the Snakemake module (see above) and you should be able to launch your workflow.
+
+## Submitting a Snakemake workflow as a Slurm job
+
+As with an interactive session, the main batch job should request the resources needed to run any subjobs marked as `localrules`.
+
+```sl
+#!/bin/bash -e
+
+#SBATCH --job-name        my job
+#SBATCH --account         nesi12345
+#SBATCH --time            01:00:00
+#SBATCH --mem             2G
+
+# load snakemake
+module load snakemake/7.32.3-gimkl-2022a-Python-3.11.3
+
+# launch snakemake workflow
+snakemake -pr --keep-going -j $SLURM_CPUS_PER_TASK all
+```
+
+## Snakemake Slurm plugin
+
+Snakemake maintains a [plugin](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html) to assist with running Snakemake with Slurm as the executor.
+This plugin supports the use of MPI jobs.
+
+## Snakemake community resources
+
+There are two main repositories for reuseable Snakemake rules and workflows.
+[Snakemake Wrappers](https://snakemake-wrappers.readthedocs.io/en/stable/) provide version controlled rules to conduct common steps in workflows.
+[Snakemake Workflows](https://snakemake.github.io/snakemake-workflow-catalog/index.html) are entire Snakemake workflows for common pipelines.
+
+
+## External references
+- [Snakemake Docs](https://snakemake.readthedocs.io/en/stable/)
+- [Snakemake Wrappers Repository](https://snakemake-wrappers.readthedocs.io/en/stable/)
+- [Snakemake Workflows Catalog](https://snakemake.github.io/snakemake-workflow-catalog/index.html)