diff --git a/tests/README.md b/tests/README.md index d41df5f..97fd602 100644 --- a/tests/README.md +++ b/tests/README.md @@ -11,30 +11,8 @@ pipelines from Acanthophis to call variants in this simulated dataset. To run this test pipeline, one must: -### Quick mode: the core pipeline using the CI suite. - -Two scripts -```bash - -## Complete version - -Either `bash setup.sh && bash test.sh`, or: - -```bash -conda env create -f environment-setup.yml -n acanthophis-demo -conda activate acanthophis-demo -# Install Acanthophis -pip install -e .. - -# Initalise Acanthophis -acanthophis-init . - -# the generate the fake dataset -snakemake --snakefile Snakefile.generate-rawdata -j 8 --use-conda - -# and run the actual test dataset -snakemake -j 8 --use-conda -``` +1. **Generate the test dataset: `bash setup.sh`**. Uses a population genetic simulation & then read simulation to generate a fake dataset. +2. **Run the tests: `bash test.sh --quick`**. Deploys the Acanthophis pipeline, and runs a slightly reduced pipeline that requires only conda (every single step of the entire pipeline can be run by omitting `--quick`, but this can take some time) To initialise your own workflow, [follow the main