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This page provides a guide to QUT users on how to install and run the nextflow nf-core/rnaseq workflow on the HPC.

Pre-requisites

• Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html )

• Basic Unix command line knowledge (example: https://researchcomputing.princeton.edu/education/external-online-resources/linux ; https://swcarpentry.github.io/shell-novice/ )

  • https://sandbox.bio/

• Familiarity with one unix text editors (example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

• Have an HPC account on QUT’s HPC compute. Apply for a new HPC account here.

• R tutorials:

  • https://girke.bioinformatics.ucr.edu/GEN242/tutorials/

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Additional details on the workflow can be found at:

Overview: https://nf-co.re/rnaseq/3.010.1

Usage: https://nf-co.re/rnaseq/3.0/usage

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#!/bin/bash -l
#PBS -N nfrna2
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00

#work on current directory (folder)
cd $PBS_O_WORKDIR

#load java and set up memory settings to run nextflow
module load java
NXF_OPTS='-Xms1g -Xmx4g'

#run the rnaseq pipeline
nextflow run nf-core/rnaseq --input samplesheet.csv \
        --outdir results \
        -r 3.10.1 \
        --genome GRCh38 \
        -profile singularity \
        --aligner star_rsem \
        --clip_r1 10 \
        --clip_r2 10 \
        --three_prime_clip_r1 12 \
        --three_prime_clip_r2 12

Submitting the job

Once you have created the folder for the run, the input.tsv file, nextflow.config, and launch.pbs, you are ready to submit.

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