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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
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.
Look for the “Access Nextflow Tower now!” email to arrive shortly after entering your address.