Prepared by the eResarch 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:
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
Note, if the running was interrupted or did not complete a particular step or you want to modify a parameter for a particular step, instead of re-running all process again nextflow enables to “-resume” the workflow.
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'
skip_cool = false
}
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.
Submit the run with this command (On Lyra)
qsub launch.pbs
Monitoring the Run
You can use the command
qstat -u $USER
To check on the jobs you are running. Nextflow will launch additional jobs during the run.
You can also check the .nextflow.log file for details on what is going on.
Finally, if you have configured the connection to the NFTower you can logon and check your run.