This repo contains scripts and pre-configured configuration files used in the analysis of clinical genomes as a part of the genomics aotearoa clinical genomics project on ESR's production network.
Descriptions of how to use these scripts/config files is described in a the following document: Standard operating procedure (SOP) for transferring, analysing and loading genomes into WDHB production scout instance
The wrapper scripts can be used to automate the process of analysing WGS clinical data on ESR's production network. There are three bash scripts which automate the following steps:
./scripts/setup_pipelines.sh- Clone human_genomics_pipeline
- Clone vcf_annotation_pipeline
- Put pipeline configuration files in place for standard pipeline runs on ESR's production cluster for this project
./scripts/check_input_files.sh- Check input files for the pipelines are downloaded and in the expected location
./scripts/deploy_pipelines.sh- Create and activate a conda environment to run the pipelines in
- Run human_genomics_pipeline
- Run vcf_annotation_pipeline
These wrapper scripts utilise user input values from the small configuration file at ./config/config.yaml.
Pre-configured configuration files and runscripts for both human_genomics_pipeline and vcf_annotation_pipeline that are standard for analysing whole genomes on ESR production network. The files are available for both single and cohort pipeline runs.
Conda environment files are available at ./envs/ to re-create conda environments with software used in this document