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Prepared by the eResearch Office, QUT.

This page provides a guide to QUT users on how to install and run the NextFlow https://nf-co.re/scrnaseq/1.1.0workflow on the HPC.

Further details on setting up, running and output of the nf-core/scrnaseq workflow can be found here:

https://nf-co.re/scrnaseq/1.1.0

https://nf-co.re/scrnaseq/1.1.0/usage

https://nf-co.re/scrnaseq/1.1.0/parameters

https://nf-co.re/scrnaseq/1.1.0/output

Install Nextflow

The nf-core/scrnaseq 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.

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

Mouse genome

http://ftp.ensembl.org/pub/release-104/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz

Mouse GTF

http://ftp.ensembl.org/pub/release-104/gtf/mus_musculus/Mus_musculus.GRCm39.104.chr.gtf.gz

Test the workflow

The nf-core/scrnaseq workflow contains a built-in dataset to test.

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


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