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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.
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.
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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:
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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.
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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.
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qsub launch.pbs |
Monitoring the Run
You can use the command
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qstat -u $USER |
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