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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.
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[[ -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
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runs
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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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