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$HOME/.nextflow/config

A sample file might look like:
(Replace $HOME with the actual path to your home folder)

process {
  executor = 'pbspro'
  beforeScript = {
    """
    source $HOME/.bashrc
    source $HOME/.profile
    """
    }
  scratch = true
  cleanup = false
}

singularity {
    cacheDir = '$HOME/.nextflow/NXF_SINGULARITY_CACHEDIR'
    autoMounts = true
}

conda {
    cacheDir = '$HOME/.nextflow/NXF_CONDA_CACHEDIR'
}

What do all these lines mean?

Lines 1-10: This process section has the defaults that ensure Nextflow can submit jobs to the PBS system on the HPC

Lines 12-15, 17-19: When Nextflow runs a pipeline, the software needed it typically delivered by a conda environment or a singularity container. Nextflow will build the environment or download the file to the pipeline’s work directory. If you run the pipeline multiple times, there is a delay while this environment is built. These settings ensure the environment is created in a central location thus speeding up subsequent runs. Nextflow does not understand the $HOME variable so please replace with your home folder. You can find this after you logon with the command 'pwd'.

Create the CACHE directories defined in the .nexflow/config above in you home space:

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You can create a suitable file for use on the QUT HPC with this.

Cut and paste the following text into your Linux command line and hit ‘enter’. This will make a few small changes to your local account so that Nextflow can run correctly.

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