Running IndexReferenceFasta-nf

We have created a very simple workflow to generate reference index files as required. The pipeline is called IndexReferenceFasta-nf. It can be used to generate indexes for:

• Samtools faidx
• GATK CreateSequenceDictionary
• BWA index

1. Download a copy of the pipeline code to your Gadi environment

A copy of this pipeline is already available at: /g/data/<project>/pipelines. But if you’d like to update that copy, run:

git clone https://github.com/Sydney-Informatics-Hub/IndexReferenceFasta-nf.git

Move into the directory, this is where you’ll be working:

cd IndexReferenceFasta-nf

2. Generate indexes

Follow the user guide to generate required indexes.

All materials copyright Sydney Informatics Hub, University of Sydney