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Prepared by the eResarch eResearch Office, QUT.

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

Further details on the workflow can be found at:

https://nf-co.re/hic

Install Nextflow

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 cextflow.config file and run a PBS pro submission script for Nextflow pipelines.

Additional information available here: https://nf-co.re/usage/installation

Getting Started

Download and run the workflow using a minimal data provided by nf-core/rnaseq. We recommend using singularity as the profile for QUT’s HPC. Other profile option can be ‘conda’. Note: the profile option ‘docker’ is not available on the HPC.

nextflow run nf-core/hic -profile test,singularity

Running the pipeline using custom data

Example of a typical command to run a RNA-seq analysis for mouse samples:

...

nextflow run nf-core/hic --input '*_R{1,2}.fastq.gz' -profile singularity -resume

Preparing to run on the HPC

To run this on the HPC a PBS submission script needs to be created.

In the folder you have created for this run create launch.pbs using a text editor (i.e., vim, nano)

Example 1: define input in launch.pbs

#!/bin/bash -l
#PBS -N nfrna2
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
RUN_NAME=run1

cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/hic --input '*_R{1,2}.fastq.gz' -name ${RUN_NAME} -profile singularity -with-dag flowchart.png | tee ${RUN_NAME}.log

Example 2: define input (i.e., FATSQ, genome file) in a separate cextflow.config file

#!/bin/bash -l
#PBS -N nfrna2
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
RUN_NAME=run1

cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/hic -name ${RUN_NAME} -profile singularity -with-dag flowchart.png | tee ${RUN_NAME}.log

nextflow.config file:

params {
  input = '/work/eresearch_bio/pwg/nextflow/hic/run1-test/data/*_R{1,2}.fastq.gz'
  fasta = '/work/eresearch_bio/pwg/nextflow/hic/run1-test/data/W303_SGD_2015_JRIU00000000.fsa'
}

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.

...

qsub launch.pbs

Monitoring the Run

You can use the command

qstat -u $USER

...