Newcastle

.github/workflows/main.yml

@@ -143,6 +143,7 @@ jobs:
           - "mssm"
           - "munin"
           - "nci_gadi"
+          - "newcastle"
           - "nu_genomics"
           - "nygc"
           - "nyu_hpc"

conf/newcastle.config

@@ -0,0 +1,42 @@
+params {
+    config_profile_description = 'Newcastle comet HPC cluster profile'
+    config_profile_contact = 'Chris Wyatt (@chriswyatt1)'
+    config_profile_url = ''
+    account = System.getenv('USER')
+}
+
+process {
+    executor = 'slurm'
+    scratch = true
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+    resourceLimits = [
+        memory: 256.GB,
+        cpus: 32,
+        time: 48.h
+    ]
+    clusterOptions = {
+        def opts = []
+        if (params.account) {
+          opts << "--account=${params.account}"
+        }
+        return opts.join(' ')
+      }
+}
+
+executor {
+    queueSize = 100
+}
+
+singularity {
+    enabled = true
+    pullTimeout = '2 h'
+    autoMounts = true
+}
+
+cleanup = true
+
+profiles {
+    debug {
+        cleanup = false
+    }
+}

docs/newcastle.md

@@ -0,0 +1,123 @@
+# nf-core/configs: Newcastle HPC Configuration
+
+Configuration for the Newcastle University HPC cluster (Slurm scheduler).
+
+## ⚠️ Important usage note
+
+**Do not run Nextflow on the login/head node.**
+
+All nf-core pipelines must be launched **from within a Slurm job** using `sbatch`. Running on the login node can overload shared resources and may result in your job being terminated. See Submit the Job section.
+
+## Setup
+
+### 1. Load Java
+
+Nextflow requires Java. On Newcastle HPC:
+
+    module load Java/17.0.6
+
+To make this persistent, add it to your `~/.bash_profile`:
+
+    # Load Java for Nextflow
+    module load Java/17.0.6
+
+### 2. Install Nextflow
+
+Install Nextflow using the official method:
+
+    curl -s https://get.nextflow.io | bash
+    chmod +x nextflow
+
+Move it to a directory in your `$PATH`:
+
+    mkdir -p $HOME/bin
+    mv nextflow $HOME/bin/
+
+Ensure `$HOME/bin` is in your `PATH` (add to `~/.bash_profile` if needed):
+
+    export PATH="$HOME/bin:$PATH"
+
+### 3. Container system (Apptainer)
+
+nf-core pipelines use containers for reproducibility.
+
+On comet, **Apptainer (formerly Singularity)** is already installed. Check with:
+
+    module avail apptainer
+
+Then load it (example):
+
+    module load Apptainer
+
+## Running pipelines
+
+### 1. Create a Slurm submission script
+
+Create a file, e.g. `run_nfcore.sh`:
+
+    #!/bin/bash
+    #SBATCH --job-name=nfcore_run
+    #SBATCH --account=YOUR_ACCOUNT
+    #SBATCH --time=24:00:00
+    #SBATCH --cpus-per-task=4
+    #SBATCH --mem=8G
+
+    module load Java/17.0.6
+    module load Apptainer
+
+    nextflow run nf-core/_pipeline_ \
+      -profile newcastle \
+      --account YOUR_ACCOUNT \
+      --outdir results \
+      -resume
+
+### 2. Submit the job
+
+    sbatch run_nfcore.sh
+
+## Configuration options
+
+### `--account`
+
+You **must** provide a Slurm account when running:
+
+    --account YOUR_PROJECT_CODE
+
+This is passed to Slurm as:
+
+    #SBATCH --account=YOUR_PROJECT_CODE
+
+## Example command to test nextflow is working (run this command, it should work!)
+
+Inside your Slurm script:
+
+    nextflow run  nf-core/fetchngs \
+      -profile newcastle,test \
+      --account bioinf_project \
+      --outdir results \
+      -resume
+
+## Example "real" command (will not work, just for demonstration)
+
+    nextflow run  nf-core/rnaseq \
+      -profile newcastle \
+      --account bioinf_project \
+      --input input_samplesheet.csv \
+      --aligner hisat2 \
+      --fasta mygenome.fasta \
+      --gtf myannotation.gtf \
+      --outdir results \
+      -resume
+
+## Troubleshooting
+
+- Jobs fail immediately → check `--account` is valid  
+- Nextflow not found → ensure `$HOME/bin` is in your `PATH`  
+- Container errors → ensure Apptainer module is loaded  
+- Jobs not starting → check Slurm queue limits (`squeue`, `sacct`)  
+
+## Support
+
+For issues with this configuration, please contact:
+
+- Chris Wyatt (@chriswyatt1)  Email: ecoflow.ucl@gmail.com  

nfcore_custom.config

@@ -298,6 +298,9 @@ profiles {
     nci_gadi {
         includeConfig "${params.custom_config_base}/conf/nci_gadi.config"
     }
+    newcastle {
+        includeConfig "${params.custom_config_base}/conf/newcastle.config"
+    }
     nu_genomics {
         includeConfig "${params.custom_config_base}/conf/nu_genomics.config"
     }