test_example

Test example of running pipeline

This subdirectory contains a test example of running the pipeline. It is used to illustrate how the pipeline works and test it.

Note that this example differs from "normal" use as it is a subdirectory of the pipeline, whereas normally the pipeline is a subdirectory (submodule) of the analysis. For this reason, the values of pipeline_path and docs in config.yaml should be changed in most other use cases as indicated in the comments in that file. However, otherwise this test example can be used as a template.

The contents are:

• config.yaml: configuration for the snakemake pipeline.
• ./results: results created by running the pipeline are here, only some are tracked in repo.
• Snakefile: top-level snakemake file.
• ./data: input data
• ./sequencing_data: sequencing data for this test example; for your pipelines, the sequencing data probably will not be stored in repo.
• .gitignore: specifies which files to track, such as only tracking selected results.

You can run the pipeline with:

snakemake --use-conda -j <n_jobs>

Note the pipeline uses the conda environment in ../environment.yml, so if you have already built that environment (named dms-vep-pipeline), you can also just run:

conda activate dms-vep-pipeline
snakemake -j <n_jobs>

The sphinx HTML documentation is rendered to https://dms-vep.github.io/dms-vep-pipeline/.