Update NCI Gadi config

.github/CODEOWNERS

@@ -7,3 +7,4 @@
 **/unsw_katana** @jscgh
 **/seadragon** @jiawku
 **/fred_hutch** @derrik-gratz
+**/nci_gadi** @georgiesamaha

conf/nci_gadi.config

@@ -1,32 +1,29 @@
 // NCI Gadi nf-core configuration profile
 params {
     config_profile_description = 'NCI Gadi HPC profile provided by nf-core/configs'
-    config_profile_contact = 'Georgie Samaha (@georgiesamaha), Matthew Downton (@mattdton)'
+    config_profile_contact = 'Georgie Samaha (@georgiesamaha), Kisaru Liyanage (@kisarur)'
     config_profile_url = 'https://opus.nci.org.au/display/Help/Gadi+User+Guide'
     project = System.getenv("PROJECT")
+    storage = "gdata/${params.project}+scratch/${params.project}"
 }
 
 // Enable use of Singularity to run containers
 singularity {
     enabled = true
     autoMounts = true
+    cacheDir = "/scratch/${params.project}/singularity"
 }
 
 // Submit up to 300 concurrent jobs (Gadi exec max)
-// pollInterval and queueStatInterval of every 5 minutes
-// submitRateLimit of 20 per minute
 executor {
     queueSize = 300
-    pollInterval = '5 min'
-    queueStatInterval = '5 min'
-    submitRateLimit = '20 min'
 }
 
 // Define process resource limits
 process {
     executor = 'pbspro'
-    project = System.getenv("PROJECT")
-    storage = 'scratch/params.project'
+    project = "${params.project}"
+    storage = "${params.storage}"
     module = 'singularity'
     cache = 'lenient'
     stageInMode = 'symlink'

docs/nci_gadi.md

@@ -12,11 +12,11 @@ Please be aware that you will need to have a user account, be a member of an Gad
 
 ### Prerequisites
 
-Before running the pipeline you will need to load Nextflow and Singularity, both of which are globally installed modules on Gadi. You can do this by running the commands below:
+Before running the pipeline you will need to load Nextflow, both of which are globally installed modules on Gadi (see `/apps`). You can do this by running the commands below:
 
 ```bash
 module purge
-module load nextflow singularity
+module load nextflow
 ```
 
 ### Execution command
@@ -32,7 +32,25 @@ nextflow run <nf-core_pipeline>/main.nf \
 
 ### Cluster considerations
 
-Please be aware that as of July 2023, NCI Gadi HPC queues **do not** have external network access. This means you will not be able to pull the workflow code base or containers if you submit your `nextflow run` command as a job on any of the standard job queues. NCI currently recommends you run your Nextflow head job either in a GNU screen or tmux session from the login node or submit it as a job to the [copyq](https://opus.nci.org.au/display/Help/Queue+Structure). See the [nf-core documentation](https://nf-co.re/docs/usage/offline) for instructions on running pipelines offline.
+#### External network access
+
+Please be aware that as of June 2025, NCI Gadi HPC compute nodes **do not** have external network access. This means you will not be able to pull the workflow code base or containers if you submit your `nextflow run` command as a job on any of the standard job queues. NCI currently recommends you run your Nextflow head job in a [persistent session](https://opus.nci.org.au/spaces/Help/pages/241926895/Persistent+Sessions) from the login node or submit it as a job to the [copyq](https://opus.nci.org.au/display/Help/Queue+Structure). See the [nf-core documentation](https://nf-co.re/docs/usage/offline) for instructions on running pipelines offline.
+
+#### Downloading containers
+
+This config requires Nextflow to use [Singularity](https://www.nextflow.io/docs/latest/container.html#singularity) to execute processes. Before a process can be executed, any nf-core pipeline you run will download that container to a local cache. This config file specifies the download and storage location with:
+
+```
+cacheDir = "/scratch/${params.project}/singularity"
+```
+
+Additionally, the project parameter is defined using the PBS environmental variable `$PROJECT`:
+
+```
+params.project = System.getenv("PROJECT")
+```
+
+#### Gadi queues and job submission
 
 This config currently determines which Gadi queue to submit your task jobs to based on the amount of memory required. For the sake of resource and cost (service unit) efficiency, the following rules are applied by this config:
 
@@ -56,7 +74,18 @@ The version of Nextflow installed on Gadi has been modified to make it easier to
 process {
     executor = 'pbspro'
     project = 'aa00'
-    storage = 'scratch/aa00+gdata/aa00'
+    storage = 'scratch/params.project'
+    ...
+}
+```
+
+Similarly, you can override the default storage location to change locations or add multiple locations by manually overriding the storage definition inside the process scope. For example:
+
+```nextflow
+process {
+    executor = 'pbspro'
+    project = System.getenv("PROJECT")
+    storage = 'scratch/aa11+gdata/aa11'
     ...
 }
 ```