.. _`bio/gatk/denoisereadcounts`:

GATK DENOISEREADCOUNTS
======================


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

Denoises read counts to produce denoised copy ratios


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/13832751133851-DenoiseReadCounts

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule denoisereadcounts:
        input:
            hdf5=["a.counts.hdf5"],
        output:
            std_copy_ratio="a.standardizedCR.tsv",
            denoised_copy_ratio="a.denoisedCR.tsv",
        log:
            "logs/gatk/denoisereadcounts.log",
        params:
            extra="",  # optional
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/denoisereadcounts"

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:**

* ``hdf5``: TSV or HDF5 file with counts from CollectReadCounts.
* ``pon``: Panel-of-normals from CreateReadCountPanelOfNormals (optional)
* ``gc_interval``: GC-content annotated-intervals from {@link AnnotateIntervals (optional)

**Output:**

* ``std_copy_ratio``: Standardized-copy-ratios file
* ``denoised_copy_ratio``: Denoised-copy-ratios file



Params
------

* ``java_opts``: 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``: 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 tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts


    pon = snakemake.input.get("pon", "")
    if pon:
        pon = f"--count-panel-of-normals {snakemake.input.pon}"


    gc_interval = snakemake.input.get("gc_interval", "")
    if gc_interval:
        gc_interval = f"--annotated-intervals {snakemake.input.gc_interval}"


    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:
        shell(
            "gatk --java-options '{java_opts}' DenoiseReadCounts"
            " --input {snakemake.input.hdf5}"
            " {pon}"
            " {gc_interval}"
            " {extra}"
            " --standardized-copy-ratios {snakemake.output.std_copy_ratio}"
            " --denoised-copy-ratios {snakemake.output.denoised_copy_ratio}"
            " --tmp-dir {tmpdir}"
            " {log}"
        )


.. |nl| raw:: html

   <br>