Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or its DOI.

0) Dependencies

You need snakemake, cyvcf2, conda and singularity to run this workflow.

conda create --name pure-faf -c conda-forge -c bioconda snakemake singularity cyvcf2
conda activate pure-faf

If you are running this workflow on an HPC environment, make sure to also install the correct executor plugin. For example:

pip install snakemake-executor-plugin-slurm

1) clone the repository

git clone https://github.com/rabiafidan/pure-faf.git

To run the workflow from command line, change the working directory.

cd path/to/pure-faf

2) configure the pipeline

Adjust options in the default config file config/config.yaml.

3) run the pipeline

Before running the complete workflow, you can perform a dry run using:

snakemake --dry-run --use-conda --use-singularity

To run the workflow locally with test files using conda and singularity:

snakemake --cores 2 --use-conda --use-singularity

you can add --no-temp flag if you need to keep every intermidate file (for debugging purposes).

You can also run the workflow on an HPC environment using an executor plugin. See snakemake documentation for more details on how to set up executor plugins. See turajlic lab usage for an example of slurm profile configuration.