Description

This repository contains a Nextflow implementation of the CgpWGS_hg38 pipeline, mutect2 and gridss.

Requirements

All tools used in this pipeline are contained in the CgpWGS_hg38 container. It can be excuted via Singularity or Docker.

• Nextflow >= 23.04 (tested version - This script makes use of DSL 2 synthax, which became the default at 22.03.0-edge)
• Reference files (As of now, the script will not check for these files and download them.)

Please do not install Singularity through conda.

Singularity must be owned by root in order to run this workflow. If you do not have access to a singularity installation owned by root try requesting to your system administrator.

How to run

1. Setup a working directory and copy the cgpWGS.nf and nextflow.config files inside it.
2. Edit the variables in 'config/params.config' to point to the appropriate directories (similar to the nextflow.config of the original pipeline). NOTE: Paths must either be absolute, or include the variable $projectDir if using paths relative to the script directory.
3. Edit the variables in config/process.config to adjust executor settings.
4. Create an input CSV table. The table must have 2 columns only: tumor file and normal file paths e.g. [./mytumor.bam,./mynormal.bam].
5. Execute nextflow run cgpWGS.nf -with-singularity <path-to-container> to execute the pipeline.

Tips

• You can execute nextflow with the flag -with-report to create an HTML resource usage report. This is useful to set resource configuration.
• If your pipeline execution is interrupted/fails, you can execute nextflow with the flag -resume to resume where you left off.