.. _`bio/cnvkit/antitarget`:

CNVKIT ANTITARGET
=================


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

Given a “target” BED file that lists the chromosomal coordinates of the tiled regions used for targeted resequencing, derive  a BED file off-target/”antitarget” regions.


**URL**: https://cnvkit.readthedocs.io/en/stable/pipeline.html#antitarget

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cnvkit_antitarget:
        input:
            bed="test.bed",
        output:
            bed="test.antitarget.bed",
        log:
            "logs/test.target.log",
        params:
            extra = "" # optional
        wrapper:
            "v3.0.1/bio/cnvkit/antitarget"

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

* ``cnvkit=0.9.10``

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

* ``bed``: bed file
* ``accessible``: sequence-accessible coordinates in chromosomes from the given reference genome

**Output:**

* ``bed``: bed file



Params
------

* ``extra``: additional parameters that will be forwarded to cnvkit antitarget




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

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

    from snakemake.shell import shell

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

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

    accessible = snakemake.input.get("accessible", "")
    if accessible:
        accessible = f"-g {accessible}"

    shell(
        "cnvkit.py antitarget "
        "{snakemake.input.bed} "
        "-o {snakemake.output.bed} "
        "{accessible} "
        "{extra} "
        "{log}"
    )


.. |nl| raw:: html

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