.. _`bio/homer/makeTagDirectory`:

HOMER MAKETAGDIRECTORY
======================


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

Create a tag directory with the HOMER suite. For more information, please see the `documentation <http://homer.ucsd.edu/homer/ngs/tagDir.html>`_.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule homer_makeTagDir:
        input:
            # input bam, can be one or a list of files
            bam="{sample}.bam",
        output:
            directory("tagDir/{sample}")
        params:
            extra=""  # optional params, see homer manual
        log:
            "logs/makeTagDir/{sample}.log"
        wrapper:
            "v3.0.1/bio/homer/makeTagDirectory"

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

* ``homer=4.11``
* ``samtools=1.18``




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2020, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"

    from snakemake.shell import shell
    import os.path as path
    import sys

    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    shell(
        "(makeTagDirectory" " {snakemake.output}" " {extra}" " {snakemake.input})" " {log}"
    )


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