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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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. In version 3.11.2, there is no option to run only quality control processes. Instead, it is possible to force the pipeline to skip reads trimming and alignment , and quantify the data using pseudo-aligned reads (pink path on the image above) - this will reduce significantly the first run of the pipeline. To execute that option, add the following flags to your nextflow run nf-core/rnaseq command: --skip_trimming, --skip_alignment and select which method should perform pseudo-alignment.
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You can experiment with different clipping options. To do this, use the nextflow run nf-core/rnaseq command with--skip_alignment like at the beginning when you were only assessing the quality of the reads, but this time, do not use--skip_trimming flag. For example, if the FastQC report suggests that you only need to clip 10 bases from the 5' end, modify the nextflow run nf-core/rnaseq in the PBS script in the following way:
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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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