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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#!/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 \ -profile singularity \ -r 3.10.1 \ --input samplesheet.csv \ --genome GRCm38 GRCh38 \ --outdir results \ --aligner star_salmon |
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. Then, we can use the PBS script below to tell the pipeline to remove a defined number of bases from the 5'-end (--clip_r1 or --clip_r2) or 3'-end (--three_prime_clip_r1 or --three_prime_clip_r2). Also, we can specify to remove ribosomal RNA as these sets of sequences are non-informative.
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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_rsemsalmon \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 2 \
--three_prime_clip_r2 2 |
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Once you have created the folder for the run, the inputsamplesheet.tsv csv file, nextflow.config, and launch.pbs, you are ready to submit.
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#delete the existing assests associated with the RNAseq pipeline: cd ~/.nextflow/assets/nf-core rm -r rnaseq/ #run again a test with the new version that you are testing, for example, version 3.10.1. See details on how to run a test above (under 'Getting Started') |
Add output folders/files
sample data
Running the pipeline using custom data
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nextflow run nf-core/rnaseq --input samplesheet.csv \
--outdir results \
-r 3.10.1 \
--genome GRCh38GRCm38 \
-profile singularity \
--aligner star_rsem \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 2 \
--three_prime_clip_r2 2 |
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nextflow run nf-core/rnaseq --input samplesheet.csv \
--outdir results \
-r 3.10.1 \
--genome GRCh38GRCm38 \
-profile singularity \
--aligner star_rsem \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 2 \
--three_prime_clip_r2 2 \
-resume |