.. _`bio/snpeff/download`:

SNPEFF DOWNLOAD
===============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/snpeff/download?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/snpeff/download

Download `snpeff <https://pcingola.github.io/SnpEff/se_introduction/>`_ DB for a given species.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule snpeff_download:
        output:
            # wildcard {reference} may be anything listed in `snpeff databases`
            directory("resources/snpeff/{reference}")
        log:
            "logs/snpeff/download/{reference}.log"
        params:
            reference="{reference}"
        # optional specification of memory usage of the JVM that snakemake will respect with global
        # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
        # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
        # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
        resources:
            mem_mb=1024
        wrapper:
            "v3.0.1/bio/snpeff/download"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``snpeff=5.2``
* ``bcftools=1.18``
* ``snakemake-wrapper-utils=0.6.2``




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2020, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    from snakemake.shell import shell
    from pathlib import Path
    from snakemake_wrapper_utils.java import get_java_opts

    java_opts = get_java_opts(snakemake)

    reference = snakemake.params.reference
    outdir = Path(snakemake.output[0]).parent.resolve()
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    shell("snpEff download {java_opts} -dataDir {outdir} {reference} {log}")


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