.. _`bio/homer/findPeaks`:

HOMER FINDPEAKS
===============


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

Find ChIP- or ATAC-Seq peaks with the HOMER suite. For more information, please see the `documentation <http://homer.ucsd.edu/homer/ngs/peaks.html>`_.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule homer_findPeaks:
        input:
            # tagDirectory of sample
            tag="tagDir/{sample}",
            # tagDirectory of control background sample - optional
            control="tagDir/control"
        output:
            "{sample}_peaks.txt"
        params:
            # one of 7 basic modes of operation, see homer manual
            style="histone",
            extra=""  # optional params, see homer manual
        log:
            "logs/findPeaks/{sample}.log"
        wrapper:
            "v3.0.1/bio/homer/findPeaks"

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)

    control = snakemake.input.get("control", "")
    if control == "":
        control_command = ""
    else:
        control_command = "-i " + control

    shell(
        "(findPeaks"
        " {snakemake.input.tag}"
        " -style {snakemake.params.style}"
        " {extra}"
        " {control_command}"
        " -o {snakemake.output})"
        " {log}"
    )


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