Newcastle

.github/workflows/main.yml

@@ -129,6 +129,7 @@ jobs:
           - "mssm"
           - "munin"
           - "nci_gadi"
+          - "newcastle"
           - "nu_genomics"
           - "nygc"
           - "nyu_hpc"

conf/newcastle.config

@@ -0,0 +1,22 @@
+params {
+    config_profile_description = 'Newcastle HPC cluster profile'
+    config_profile_contact = 'Chris Wyatt (@chriswyatt1), Fernando Duarte (@FernandoDuarteF)'
+    config_profile_url = ''
+}
+
+executor {
+    name = 'slurm'
+}
+
+process {
+    scratch = true
+    errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' }
+    queue   = 'defq'                    // maps to `#SBATCH -p defq`
+    clusterOptions = '--account=DESIM'  // maps to `#SBATCH -A DESIM`
+}
+
+singularity {
+    enabled = true
+    pullTimeout = '2 h'
+    autoMounts = true
+}

docs/newcastle.md

@@ -0,0 +1,46 @@
+# nf-core/configs: Newcastle HPC Configuration
+
+Configuration for the Newcastle high performance computing (HPC) cluster.
+
+## Setup
+
+To install nextflow we first need to get the prequisite java from module avail:
+
+`module load Java/17.0.6`
+
+Then installing Nextflow using the standard install options:
+https://www.nextflow.io/docs/latest/install.html
+
+`curl -s https://get.nextflow.io | bash`
+
+Make Nextflow executable:
+
+`chmod +x nextflow`
+
+Then move Nextflow into an executable path. For example:
+
+`mkdir -p $HOME/bin/`
+`mv nextflow $HOME/bin/`
+
+To ensure this works every time you login to the cluster, put inside your `~/.bash_profile` the java install:
+
+`nano ~/.bash_profile`
+
+Then paste in the line for the java install:
+
+```
+#Java module add v17:
+module load Java/17.0.6
+```
+
+Exit nano with, control-X, then y to save, then enter to confirm
+
+## Run
+
+To use this profile, simply pass Nextflow the -profile newcastle flag eg.
+
+```bash
+nextflow run nf-core/_pipeline_ -profile newcastle --outdir results
+```
+
+In case of issues, please feel free to reach out to one of the maintainers (Chris Wyatt or Fernando Duarte) at ecoflow.ucl@gmail.com . We are based at UCL, but helped set up this config, and are happy to help.

nfcore_custom.config

@@ -295,6 +295,9 @@ 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"
     }