.. _`bio/refgenie`:

REFGENIE
========


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

Deploy biomedical reference datasets via refgenie.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule obtain_asset:
        output:
            # the name refers to the refgenie seek key (see attributes on http://refgenomes.databio.org)
            fai="refs/genome.fasta"
            # Multiple outputs/seek keys are possible here.
        params:
            genome="human_alu",
            asset="fasta",
            tag="default"
        wrapper:
            "v3.0.1/bio/refgenie"

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
---------------------

* ``refgenie=0.12.1``
* ``refgenconf=0.12.2``




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2019, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    import os
    import refgenconf

    genome = snakemake.params.genome
    asset = snakemake.params.asset
    tag = snakemake.params.tag

    conf_path = os.environ["REFGENIE"]

    rgc = refgenconf.RefGenConf(conf_path, writable=True)

    # pull asset if necessary
    gat, archive_data, server_url = rgc.pull(genome, asset, tag, force=False)

    for seek_key, out in snakemake.output.items():
        path = rgc.seek(genome, asset, tag_name=tag, seek_key=seek_key, strict_exists=True)
        os.symlink(path, out)


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