Clinical Genomics Uppsala rare disease pipeline for Illumina whole genome sequence data.
https://poirot-rd-wgs.readthedocs.io/en/latest/
This ReadMe is only a brief introduction, please refer to ReadTheDocs for the latest documentation and a more detailed description of the pipeline.
This pipeline is created to run on Illumina whole genome sequence data to call germline variants.
The workflow repository contains a dry run test of the pipeline in .tests/integration which can be run like so:
$ cd .tests/integration
$ snakemake -n -s ../../workflow/Snakefile --configfile config/config.yaml 🚀 Usage
To use this run this pipeline the requirements in requirements.txt must be installed. It is most straightforward to install the requirements inside a python virtual environment created with the python venv module. The sample.tsv, units.tsv, resources.yaml, and config.yaml files need to be available in the current directory (or otherwise specified in config.yaml). You always need to specify the config-file either in the profile yaml file or in the snakemake command. To run the pipeline:
$ snakemake --profile /path/to/snakemakeprofile --configfile config.yaml -s /path/to/poirot_rd_wgs/workflow/Snakefile