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Snakemake workflow: Parallel Freebayes analysis

Snakemake Build Status

Variant frequency analysis in population with low coverage per sample

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description, covering the purpose and domain. Insert your code into the respective folders, i.e. scripts, rules and envs. Define the entry point of the workflow in the Snakefile and the main configuration in the config.yaml file.

The workflow is written using Snakemake.

Dependencies are installed using Bioconda where possible.

Setup environment and run workflow

  1. Clone workflow into working directory

    git clone <repo> <dir> cd <dir>

  2. Download input data

    Copy data from URL to data directory

  3. Edit config as needed

    cp config.yaml.sample config.yaml nano config.yaml

  4. Install dependencies into isolated environment

    conda env create -n <project> --file environment.yaml

  5. Activate environment

    source activate <project>

  6. Execute workflow

    snakemake -n

Running workflow on gen-comp1

snakemake --cluster-config cetus_cluster.yaml \
          --drmaa " --cpus-per-task={cluster.n} --mem={cluster.memory} --qos={cluster.qos}" \
          --use-conda -w 60 -rp -j 1000

Testing

Tests cases are in the subfolder .test. They should be executed via continuous integration with Travis CI.