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Copy 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.

[[ -d $HOME${HOME}/.nextflow ]] || mkdir -p $HOME${HOME}/.nextflow
cat <<EOF > $HOME${HOME}/.nextflow/config
singularity {
    cacheDir = '$HOME${HOME}/.nextflow/NXF_SINGULARITY_CACHEDIR'
    autoMounts = true
}
conda {
    cacheDir = '$HOME${HOME}/.nextflow/NXF_CONDA_CACHEDIR'
}
process {
  executor = 'pbspro'
  scratch = false
  cleanup = false
}
EOF

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• Lines 1-5 are typical PBS system commands here the name of the job is MyNextflowRun, 2 CPUS and 4gb of ram is selected, and the job will run for 24 hours. This is the total time for the pipeline run - it may take days or weeks depending on how much data and the pipeline.

• Line 6 is to ensure the Java environment is available (Nextflow needs Java to run)

• Line 7 tells Nextflow how much RAM to use

• Line 8 runs Nextflow.

To see the output of Nextflow while running as a job, you can use the Nextflow Tower.

Using the Nextflow Tower

Nextflow Tower allow monitoring of Nextflow runs. To use the NFTower, please visit

https://nftower.qut.edu.au or the BioCommons: https://tower.services.biocommons.org.au/

(Control-Click this to open in a new Window)

There are no passwords for the Tower, instead, you use a link sent to your email.

Look for the Sign in button (Top Right) then provide your email address.

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• Nextflow

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