This package contains a simple command line helper for running Snakemake workflows on a high performance computing cluster using sensible default values.
pip install git+https://github.com/lumc-pgx/pipe-runner.git
Usage: pipe-runner [OPTIONS] [ADDITIONAL_ARGS]...
Options:
-s, --snakefile PATH path to the snakemake file to be run
-d, --directory PATH Directory for pipeline output
-e, --extraconfig TEXT string containing additional config parameters
-c, --configfile PATH path to an additional config file containing run-
specific parameters
-cl, --clusterconfig PATH path to the cluster configuration file
-r, --retries INTEGER Number of times to retry a failed pipeline stage
-h, --help Show this message and exit.
Example:
pipe-runner -s Snakefile -d output_dir -c run_config.yaml -cl cluster_settings.yaml
Modify the run_config.yaml and cluster_settings.yaml according to the location of your data and run parameters.
The CYP2D6_locus_config.yaml is an example of locus definition file indicated in the run_config.yaml and should be changed according to the gene of interest.
The output of the pipeline includes the following folders
- Annotation
- Haplotyping
- Phasing
- Structural variation
- Summary
- Variant calling