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nf-core/configs: NCI Gadi proteinfold specific configuration

Extra specific configuration for proteinfold pipeline

Usage

To use, run the pipeline with -profile nci_gadi.

This will download and launch the proteinfold specific nci_gadi.config which has been pre-configured with a setup suitable for the NCI Gadi HPC cluster.

Example: nextflow run nf-core/proteinfold -profile nci_gadi

proteinfold specific configurations for NCI Gadi

Specific configurations for NCI Gadi has been made for proteinfold.

Project accounting

As described here the config uses the PBS environmental variable $PROJECT to assign a project code to all task job submissions for billing purposes. If you are a member of multiple Gadi projects, you should confirm which project will be charged for your pipeline execution. You can do this using:

echo $PROJECT

The version of Nextflow installed on Gadi has been modified to make it easier to specify resource options for jobs submitted to the cluster. See NCI's Gadi user guide for more details. You can manually override the $PROJECT specification by editing your local copy of the nci_gadi.config and replacing $PROJECT with your project code. For example:

process {
    project = '<abc>'
    storage'scratch/<abc>+gdata/<abc>'
    ...
}

or export specification manually

export $PROJECT = '<abc>'

Storage considerations

When running proteinfold on NCI Gadi it is expected that all your data will be contained within the projects /scratch and /g/data directories, as specified in $PROJECT . However, if you are working across multiple project codes, you will need to manually edit this line in the nci_gadi.config to reflect this:

storage = "scratch/<abc>+gdata/<def>"

Alternatively, you can use the --storage_account "scratch/abc+gdata/def" parameter to specify access to storage as required.

⚠️ Expected Warnings

When running the pipeline, you may encounter the following warnings:

WARN: The following invalid input values have been detected:

* --storage_account: scratch/abc+gdata/def
* --project: abc

These warnings can be safely ignored. The parameters are required for job allocations and billing purposes on NCI Gadi, but they do not affect execution.