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You can create a suitable file for use on the QUT HPC with this.
Cut 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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However, it is good practice and much safer to submit a job on the HPC to run Nextflow on your pipeline. A job file (called launch.pbs) might look like:
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#!/bin/bash -l #PBS -N MyNextflowRun #PBS -l select=1:ncpus=2:mem=6gb #PBS -l walltime=24:00:00 cd $PBS_O_WORKDIR module load java NXF_OPTS='-Xms1g -Xmx4g' nextflow run nf-core/rnaseq |
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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)
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