.. _`bio/epic/peaks`:

EPIC
====


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

Find broad enriched domains in ChIP-Seq data with epic



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule epic:
        input:
          treatment = "bed/test.bed",
          background = "bed/control.bed"
        output:
          enriched_regions = "epic/enriched_regions.csv", # required
          bed = "epic/enriched_regions.bed", # optional
          matrix = "epic/matrix.gz" # optional
        log:
            "logs/epic/epic.log"
        params:
          genome = "hg19", # optional, default hg19
          extra="-g 3 -w 200" # "--bigwig epic/bigwigs"
        threads: 1 # optional, defaults to 1
        wrapper:
            "v3.0.1/bio/epic/peaks"

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.


Notes
-----

* All/any of the different bigwig options must be given as extra parameters


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

* ``epic=0.2.12``
* ``pandas=1.1.5``

Input/Output
------------
**Input:**

* ``treatment``: chip .bed(.gz/.bz) files
* ``background``: input .bed(.gz/.bz) files

**Output:**

* ``enriched_regions``: main output file with enriched peaks
* ``bed``: (optional) contains much of the same info as enriched_regions but in a bed format, suitable for viewing in the UCSC genome browser or downstream use with bedtools
* ``matrix``: (optional) a gzipped matrix of read counts



Params
------

* ``extra``: additional parameters

* ``log``: (optional) file to write the log output to




Authors
-------

* Endre Bakken Stovner


Code
----

.. code-block:: python

    __author__ = "Endre Bakken Stovner"
    __copyright__ = "Copyright 2017, Endre Bakken Stovner"
    __email__ = "endrebak85@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")
    threads = snakemake.threads or 1

    treatment = snakemake.input.get("treatment")
    background = snakemake.input.get("background")

    # Executed shell command
    enriched_regions = snakemake.output.get("enriched_regions")

    bed = snakemake.output.get("bed")
    matrix = snakemake.output.get("matrix")

    if len(snakemake.log) > 0:
        log = snakemake.log[0]

    genome = snakemake.params.get("genome")

    cmd = "epic -cpu {threads} -t {treatment} -c {background} -o {enriched_regions} -gn {genome}"

    if bed:
        cmd += " -b {bed}"
    if matrix:
        cmd += " -sm {matrix}"
    if log:
        cmd += " -l {log}"

    cmd += " {extra}"

    shell(cmd)


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