This workflow can be used as module within a super-project by installing it as a git submodule.
git submodule add git@github.com:swarbricklab/genotyping.git modules/genotyping
This will create a clone of this repo at modules/genotyping within the super project.
If you are working on a project where this workflow has been installed as a submodule, note that submodules are not checked out by default when you git clone the super-project.
You can include submodules by cloning as follows:
git clone --recurse-submodules {repository_url}
If you forget to do this while cloning, then you can initialise all submodules and bring them up to date with the following command:
git submodule update --init --recursive
Alternatively, you can run
dt_clone {repository_url}
The dt_clone command is available within DVC environments on NCI.
This command checks out submodules and sets the DVC cache to a shared location.
To evaluate the workflow on its own -- for example to run the bundled public test dataset -- clone it directly, including its submodules (it pulls in the shared profiles/global profile):
git clone --recurse-submodules git@github.com:swarbricklab/genotyping.git
Then fetch the inputs and run the test as described in Running the workflow -- see the test-run instructions there and prep.sh --what all --configfile config/test.yaml.