.. _`bio/homer/mergePeaks`:

HOMER MERGEPEAKS
================


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

Merge ChIP-Seq peaks from multiple peak files. For more information, please see the `documentation <http://homer.ucsd.edu/homer/ngs/mergePeaks.html>`_. Please be aware that this wrapper does not yet support use of the ``-prefix`` parameter.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule homer_mergePeaks:
        input:
            # input peak files
            "peaks/{sample1}.peaks",
            "peaks/{sample2}.peaks"
        output:
            "merged/{sample1}_{sample2}.peaks"
        params:
            extra="-d given"  # optional params, see homer manual
        log:
            "logs/mergePeaks/{sample1}_{sample2}.log"
        wrapper:
            "v3.0.1/bio/homer/mergePeaks"

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``




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)


    class PrefixNotSupportedError(Exception):
        pass


    if "-prefix" in extra:
        raise PrefixNotSupportedError(
            "The use of the -prefix parameter is not yet supported in this wrapper"
        )

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


.. |nl| raw:: html

   <br>