IndexReferenceFasta-nf

===========

Description
Diagram
User guide
Benchmarking
Workflow summaries
Additional notes
Help/FAQ/Troubleshooting
Acknowledgements/citations/credits

Description

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

Diagram

User guide

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 --samtools, --bwa, and/or --gatk flags. All are optional. Run the pipeline with:

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

Benchmarking

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

task_id	hash	native_id	name	status	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
3	27/33fffc	131621	samtools_index	COMPLETED	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	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	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

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
bio.tools	NA
BioContainers	NA
bioconda	NA

Component tools

samtools/1.15.1
gatk/4.2.6.1
bwa/0.7.17

Required (minimum) inputs/parameters

A reference genome file in fasta format.

Additional notes

Help/FAQ/Troubleshooting

Acknowledgements/citations/credits

Authors

Georgie Samaha (Sydney Informatics Hub, University of Sydney)

Acknowledgements

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

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.