🚧🚨 Under development 🚨🚧

GRIDSS/PURPLE/LINX pipeline

A Nextflow pipeline for the GRIDSS/PURPLE/LINX (GPL) toolkit used to call and annotate structural variants. The GPL toolkit is comprised of distinct but closely integrated pieces of software that together leverage both copy number alterations and structural variants detected in short reads to improve calling accuracy and sensitivity.

This pipeline is currently targeted to bcbio outputs.

For AWS users: please see this README.md for AWS usage and other info.

Table of contents

• Installation
• Usage
• Outputs
• Requirements
• Reference data
• License

Installation

The GPL toolkit contains many pieces of software with numerous dependencies. It is recommended using the pre-built Docker image with the Nextflow pipeline to avoid a laborious installation process. If you cannot or do not want to use Docker, please see the Requirements section for further information.

These installation instructions assume you'll be using the pre-built Docker image with the Nextflow pipeline. Docker must be installed prior to usage.

# Clone repo
git clone https://github.com/umccr/gridss-purple-linx-nf.git && cd gridss-purple-linx-nf/

# Create a Conda environment and install Nextflow if required
conda create -p $(pwd -P)/conda_env/ -y -c bioconda -c conda-forge nextflow
conda activate conda_env/

# Test that you're good to go
./main.nf -help

Usage

First you'll need to obtain reference data as described here. Then create a configuration file (for an example see: nextflow.config). To execute the pipeline:

./main.nf

Outputs

Directories

Name	Contents
gridss/	GRIDSS final output
gripss/	Filtered SVs
linx_annotation/	Data for clustered and annotated SVs
linx_visualiser/	Plots for clustered and annotated SVs
nextflow/	Pipeline config, logs, and reports
nextflow/work/	Intermediary work files
purple/	CNA calls, purity, ploidy

Useful files

Name	Description
<tumor_name>_linx.html	gpgr LINX Rmd report
linx_annotation/*tsv	Grouped and annotated SV events
linx_visualiser/plot/*png	SV event plots
purple/plot/*png	Purity, ploidy, circos, etc plots
purple/<tumor_name>.<vcf_type>.vcf.gz	VCF provided to and annotated by PURPLE
gridss/sv_annotated.vcf.gz	Final GRIDSS output SV VCF
gripps/<prefix>.gripps.filtered.vcf.gz	Hard filtered SV VCF
gripps/<prefix>.gripss.vcf.gz	Soft filtered SV VCF
nextflow/nextflow_log.txt	Pipeline log file
nextflow/nextflow.config	Pipeline configuration used in run
nextflow/reports/timeline.html	Stage execution durations as a timeline

Requirements

Software versions only indicate what is currently in use rather than strict requirements

Pipeline

Assumes the pipeline will be executed using the provided Docker image

• Docker (v20.10.11)
• Nextflow (v21.04.3)

GPL toolkit

• AMBER (v3.7)
• COBALT (v1.11)
• GRIDSS (v2.13.2)
• GRIPSS (v2.0)
• PURPLE (v3.3)
• LINX (v1.20)

Reference data

The GPL toolkit requires a number of reference files. These can be obtained from the HMF Nextcloud instance here. Alternatively, I've precompiled the required files on S3, located at s3://umccr-refdata-dev/gpl-nf/.

License

Software and code in this repository are under GNU General Public License v3.0 unless otherwise indicated.