Prepared by the eResearch Office, QUT.
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The nf-core/rnaseq workflow requires Nextflow to be installed in your account on the HPC. Find details on how to install and test Nextflow here. Prepare a nextflow.config file and run a PBS pro submission script for Nextflow pipelines.
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However, before you do it, consider running the version of the pipeline that will preprocess reads and then adjust the Trim Galore options (described below).
Reads preprocessing
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We recommend running the nextflow nf-core/rnaseq pipeline once and then assessing the fastqc results folder to assess if sequence biases are present in the 5'-end and 3'-end ends of the sequences. Version 3.12.0 allows running the pipeline to do quality assessment only, without any alignment, read counting or trimming. To execute that option, add the following flags to your nextflow run nf-core/rnaseq command: --skip_trimming, --skip_alignment and --skip_pseudo_alignment.
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Finally, if you have configured the connection to the NFTower, you can log on and check your run.
Troubleshooting
Add output folders/files
sample data
If the running was interrupted or you did not complete a particular step, or you want to modify a parameter for a particular step, instead of re-running all processes again, nextflow enables you to “-resume” the workflow.
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