Updated user documentation and user guide links for SHU BMRC

conf/shu_bmrc.config

@@ -14,7 +14,7 @@ params {
 
     config_profile_description = 'Sheffield Hallam Universty - BMRC HPC'
     config_profile_contact = 'Dr Lewis A Quayle (l.quayle@shu.ac.uk)'
-    config_profile_url = 'https://openflighthpc.org/latest/docs/'
+    config_profile_url = 'https://bmrc-hpc-documentation.readthedocs.io/en/latest/'
 
 }
 

docs/shu_bmrc.md

@@ -1,13 +1,88 @@
 # nf-core/configs: Sheffield Hallam University BMRC Cluster Configuration
 
-## Using the Institutional Configuration Profile
+This document provides guidelines for using nf-core pipelines on Sheffield Hallam University's BMRC High-Performance Computing (HPC) cluster. The custom configuration file for this cluster enables optimised resource usage and workflow compatibility within the BMRC HPC environment, facilitating efficient execution of nf-core workflows.
 
-To use [`shu_bmrc.config`](../conf/shu_bmrc.config), run nextflow with an nf-core pipeline using `-profile shu_bmrc` (note the single hyphen).
+---
 
-This will download and launch [`shu_bmrc.config`](../conf/shu_bmrc.config) which has been pre-configured with a setup suitable for the BMRC cluster and will automatically load the appropriate pipeline-specific configuration file.
+## Table of Contents
 
-## Running nf-core Pipelines on the BMRC Cluster
+1. [Introduction](#introduction)
+2. [Requirements](#requirements)
+3. [Configuration Details](#configuration-details)
+4. [Usage](#usage)
+5. [Troubleshooting](#troubleshooting)
+6. [Support and Contact](#support-and-contact)
 
-A detailed guide to setting up Nextflow and nf-core and running pipelines on the BMRC Cluster is available here: [Running Nextflow with nf-core Pipelines on SHU BMRC Cluster](https://github.com/lquayle88/nfcore_on_shu_bmrc)
+---
 
-If you have any questions or issues not addressed by this guide, please contact: [l.quayle@shu.ac.uk](mailto:l.quayle@shu.ac.uk)
+## Introduction
+
+This configuration file is specifically designed for running nf-core workflows on the BMRC HPC cluster at **Sheffield Hallam University**. The configuration integrates optimal resource parameters and scheduling policies to ensure efficient job execution on the cluster, aligning with internal HPC policies and specifications.
+
+The cluster configuration:
+
+- **Location**: BMRC HPC Cluster at Sheffield Hallam University
+- **Contact**: Dr Lewis A Quayle ([l.quayle@shu.ac.uk](mailto:l.quayle@shu.ac.uk))
+- **Documentation**: [BMRC HPC Documentation](https://bmrc-hpc-documentation.readthedocs.io/en/latest/)
+
+## Requirements
+
+To use this configuration, you must have:
+
+- **Access to BMRC HPC**: Ensure your user account is enabled for HPC access at Sheffield Hallam University. The **GlobalProtect VPN** is required for remote access. For setup instructions, refer to [SHU VPN Guide](https://www.shu.ac.uk/digital-skills/programs-and-applications/virtual-private-network-vpn).
+- **Nextflow**: Version 20.10.0 or later is recommended for optimal compatibility.
+
+For a detailed guide to setting up Nextflow and running nf-core pipelines on the BMRC cluster, refer to [Running nf-core Pipelines on SHU BMRC Cluster](https://bmrc-hpc-documentation.readthedocs.io/en/latest/nfcore/index.html).
+
+## Configuration Details
+
+The configuration has been tailored for the BMRC HPC, providing preset values for CPUs, memory, and scheduling to align with HPC policies.
+
+### Core Configuration
+
+- **Cluster Scheduler**: `slurm`
+- **Max Retries**: 2 (automatically reattempts failed jobs)
+- **Queue Size**: 50 jobs
+- **Submit Rate Limit**: 1 job per second
+
+### Resource Allocation
+
+Each nf-core workflows will automatically receive the following default resource maxima:
+
+| Resource | Setting   |
+| -------- | --------- |
+| CPUs     | 64        |
+| Memory   | 1007 GB   |
+| Time     | 999 hours |
+
+### Container Support
+
+The configuration supports Apptainer for containerised workflows, with automatic mounting enabled, allowing seamless access to necessary filesystems within containers.
+
+### Cleanup
+
+Intermediate files from successful runs will be automatically deleted to free up storage.
+
+## Usage
+
+To launch an nf-core pipeline on the BMRC cluster using the `shu_bmrc` profile:
+
+```bash
+nextflow run nf-core/<pipeline_name> -profile shu_bmrc
+```
+
+## Troubleshooting
+
+If you encounter issues, ensure you have:
+
+- Followed the user guide on the BMRC HPC documentation site (see below).
+- Specified the correct profile (`shu_bmrc`) for the cluster.
+- Checked for sufficient permissions on the BMRC HPC cluster.
+- Verified that Apptainer is enabled and accessible within your environment.
+
+## Support and Contact
+
+For support or questions, contact:
+
+- **Primary Contact**: Dr Lewis A Quayle ([l.quayle@shu.ac.uk](mailto:l.quayle@shu.ac.uk))
+- **BMRC HPC Documentation**: [Link](https://bmrc-hpc-documentation.readthedocs.io/en/latest/)