This is an example workflow using the targets R package. It is based on the Data Carpentry Variant Calling Workflow lesson.
Docker is used to run various programs. The docker daemon needs to be running so that containers can be launched. conda is used to maintain the environment for running Docker.
Restore the conda environment used by this project, called vcf-example-env:
conda env create -f environment.yml
Enter the environment:
conda activate vcf-example-env
The vcf-example-env environment includes R, which is used to run the workflow. The renv R package is used to maintain packages. The first time the analysis is run, you will need to restore the packages with renv:
Rscript -e 'renv::restore()'
Activate the vcf-example-env environment, then run Rscript -e 'targets::tar_make()'.