VarFish Workflow: Validation

This Snakemake-based workflow is used for running the validation of VarFish Server.

Installing

As a prerequisite, install conda and mamba package. Activate conda.

$ mamba env create -n varfish-wf-validation --file environment.yaml
$ conda activte varfish-wf-validation

Configuring

Copy config/main.yml.example to config/main.yml and adjust paths.

You will need a number of files for that.

TODO: document how to properly setup

Running

First, kickoff the import.

# cd workflow
workflow # snakemake --cores=10 -p import-started/GRCh37/.done

Then, wait until all import jobs have completed. Future versions will allow you to wait automatically.

Then, kickoff the querying and validation.

workflow # snakemake --cores=10 -p validation/GRCh37/all_statuses.txt