• Description
• Diagram
• User guide
• Benchmarking
• Workflow summaries
  • Metadata
  • Component tools
  • Required (minimum) inputs/parameters
• Additional notes
• Help/FAQ/Troubleshooting
• Acknowledgements/citations/credits

This is a flexible pipeline for generating common reference genome index files for WGS data analysis. IndexReferenceFasta-nf is a Nextflow (DSL2) pipeline that runs the following tools using either Docker or Singularity to run containerised software for:

• Samtools faidx
• BWA index
• GATK CreateSequenceDictionary

1. Set up

Clone this repository by running:

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

2. Generate indexes

Users can specify which index files to create by using the --bwa, and/or --gatk flags. GATK and BWA indexes are optional, while Samtools is run by default. Run the pipeline with:

nextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile <nimbus/gadi/standard>

If you are running the pipeline on NCI Gadi or Pawsey's Nimbus cloud you should specify this with the -profile flag at runtime. This will allow you to use Singularity to run containers at Gadi and Docker to run the containers at Nimbus.

Standard

To run the pipeline on your own system, you will need to have Nextflow installed. You can adjust the standard.config configuration file depending on your own system needs. Currently it runs containers with Singularity. You can test your customised config file using the test fasta available in testData.

To run the pipeline with the standard.config, run the following:

nextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile standard 

NCI Gadi HPC

To run the pipeline at NCI Gadi, first load the Gadi-specific Nextflow installation:

module load nextflow

Then run the pipeline:

nextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile gadi --whoami <us1111> --pbs_account <aa00>

Pawsey Nimbus cloud

To run the pipeline at Pawsey's Nimbus cloud:

nextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile nimbus

Infrasturcture-specific config files can be found in config/

• samtools/1.15.1
• gatk/4.3.0.0
• bwa/0.7.17

• A reference genome file in fasta format.

• A subset fasta file for testing is available in testData/

• Georgie Samaha (Sydney Informatics Hub, University of Sydney)

• This pipeline was built using the Nextflow DSL2 template.
• Documentation was created following the Australian BioCommons documentation guidelines.

Acknowledgements (and co-authorship, where appropriate) are an important way for us to demonstrate the value we bring to your research. Your research outcomes are vital for ongoing funding of the Sydney Informatics Hub and national compute facilities. We suggest including the following acknowledgement in any publications that follow from this work:

The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney and the Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia.