.. _`bio/gatk/learnreadorientationmodel`:

GATK LEARNREADORIENTATIONMODEL
==============================


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

Get the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter

**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570329571227-LearnReadOrientationModel

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_gatk_learnreadorientationmodel:
        input:
            f1r2="f1r2.tar.gz",
        output:
            "artifacts_prior.tar.gz",
        resources:
            mem_mb=1024,
        params:
            extra="",
        log:
            "learnreadorientationbias.log",
        wrapper:
            "v3.0.1/bio/gatk/learnreadorientationmodel"

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
-----

* The `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).
* The `extra` param allows for additional program arguments.


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

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

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

* ``f1r2``: Path to one or multiple f1r2 files

**Output:**

* Path to tar.gz of artifact prior tables




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    #!/usr/bin/env python3
    # coding: utf-8

    """Snakemake wrapper for GATK4 LearnReadOrientationModel"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2022, Dayris Thibault"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

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

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    f1r2 = "--input "
    if isinstance(snakemake.input["f1r2"], list):
        # Case user provided a list of archives
        f1r2 += "--input ".join(snakemake.input["f1r2"])
    else:
        # Case user provided a single archive as a string
        f1r2 += snakemake.input["f1r2"]


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' LearnReadOrientationModel"  # Tool and its subprocess
            " {f1r2}"  # Path to input mapping file
            " {extra}"  # Extra parameters
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output[0]}"  # Path to output vcf file
            " {log}"  # Logging behaviour
        )


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