main @ ac2d99e

Workflow Type: Nextflow




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 Singularity containers:

  • Samtools faidx
  • BWA index
  • GATK CreateSequenceDictionary


User guide

1. Set up

Clone this repository by running:

git clone
cd IndexReferenceFasta-nf

2. Generate indexes

Users can specify which index files to create by using the --samtools, --bwa, and/or --gatk flags. All are optional. Run the pipeline with:

nextflow run /path/to/ref.fasta --bwa --samtools --gatk 


Human hg38 reference assembly @ Pawsey's Nimbus (NCPU/task = 1)

task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
3 27/33fffc 131621 samtools_index COMPLETED 0 55:44.9 12.2s 12s 99.20% 6.3 MB 11.8 MB 3 GB 19.1 KB
1 80/f03e46 131999 gatk_index COMPLETED 0 55:46.7 22.6s 22.3s 231.90% 3.8 GB 37.1 GB 3.1 GB 726 KB
2 ea/e29535 131594 bwa_index COMPLETED 0 55:44.9 1h 50m 16s 1h 50m 15s 99.50% 4.5 GB 4.5 GB 12.1 GB 8.2 GB

Workflow summaries


metadata field workflow_name / workflow_version
Version workflow_version
Maturity under development
Creators Georgie Samaha
Source NA
License GPL-3.0 license
Workflow manager NextFlow
Container None
Install method Manual
GitHub Sydney-Informatics-Hub/IndexReferenceFasta-nf NA
BioContainers NA
bioconda NA

Component tools

  • samtools/1.15.1
  • gatk/
  • bwa/0.7.17

Required (minimum) inputs/parameters

  • A reference genome file in fasta format.

Additional notes




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


Cite us to support us!

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.

Version History

main @ ac2d99e (earliest) Created 12th Oct 2022 at 03:34 by Georgina Samaha

fixed readme formatting

Frozen main ac2d99e
help Creators and Submitter
Samaha, G. (2022). IndexReferenceFasta-nf. WorkflowHub.

Views: 1660   Downloads: 123

Created: 12th Oct 2022 at 03:34

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