Snakemake docs page (#909)

Closes #895

---------

Co-authored-by: [email protected] <[email protected]>
Co-authored-by: Cal <[email protected]>

Author: jen-reeve

docs/Software/Available_Applications/Cylc.md

@@ -1,6 +1,7 @@
 ---
 created_at: '2022-08-03T21:35:50Z'
-tags: []
+tags: 
+  - workflow
 ---
 
 !!! note "Alternatives"

docs/Software/Available_Applications/snakemake.md

@@ -0,0 +1,67 @@
+---
+created_at: 2025-11-10
+tags: 
+  - workflow
+---
+
+!!! note "Alternatives"
+    See [Nextflow](Nextflow.md) and [Cylc](Cylc.md) for other possible choices of workflow engine.
+
+[//]:snakemake.md> (APPS PAGE BOILERPLATE START)
+{% set app_name = "snakemake" %}
+{% set app = applications[app_name] %}
+{% include "partials/app_header.html" %}
+[//]:snakemake.md> (APPS PAGE BOILERPLATE END)
+
+## 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 in an interactive Slurm session
+
+Request an interactive Slurm session with the resources required to run all sub-jobs labeled as `localrules`:
+
+```sl
+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 workflow as a Slurm job
+
+As with an interactive session, the main batch job should request the resources needed to run any sub-jobs 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/{{app.default}}
+
+# launch snakemake workflow
+snakemake -pr --keep-going -j $SLURM_CPUS_PER_TASK all
+```
+
+## 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.
+
+## Community resources
+
+There are two main repositories for reusable 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.
+
+!!! note "Other Resources"
+    - [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)