.. _`bio/gatk/callcopyratiosegments`:

GATK CALLCOPYRATIONSEGMENTS
===========================


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

Calls copy-ratio segments as amplified, deleted, or copy-number neutral


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/13832751795227-CallCopyRatioSegments

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule call_copy_ratio_segments:
        input:
            copy_ratio_seg="a.cr.seg",
        output:
            called_copy_ratio_seg="a.called.seg",
            igv_seg="a.called.igv.seg",
        log:
            "logs/gatk/call_copy_ratio_segments.log",
        params:
            #prefix="a.den.test",
            extra="",  # optional
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/callcopyratiosegments"

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

* ``gatk4=4.4.0.0``
* ``snakemake-wrapper-utils=0.6.2``

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

* ``copy_ratio_seg``: cr.seq file from ModelSegments

**Output:**

* ``copy_ratio_seg``: called copy ratio segments file
* ``igv_seg``: CBS formatted igv.seg file, optional



Params
------

* ``java_opts``: param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).

* ``extra``: param allows for additional program arguments.




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2023, Patrik Smed"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"

    import os
    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts


    input_copy_ratio_seg = snakemake.input.copy_ratio_seg

    called_copy_ratio_seg = snakemake.output.called_copy_ratio_seg

    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    with tempfile.TemporaryDirectory() as tmpdir:
        outputfile_call = os.path.join(tmpdir, "temp.seq")
        outputfile_igv = os.path.join(tmpdir, "temp.igv.seg")
        shell(
            "gatk --java-options '{java_opts}' CallCopyRatioSegments"
            " -I {input_copy_ratio_seg}"
            " -O {outputfile_call}"
            " --tmp-dir {tmpdir}"
            " {extra}"
            " {log}"
        )
        shell("cp {outputfile_call} {called_copy_ratio_seg}")
        if snakemake.output.get("igv_seg", None):
            shell("cp {outputfile_igv} {snakemake.output.igv_seg}")


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