.. _`bio/cnvkit/target`:

CNVKIT TARGET
=============


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

Prepare a BED file of baited regions for use with CNVkit.


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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cnvkit_targetl:
        input:
            bed="test.bed",
            annotate="refflat-mini.txt",
        output:
            bed="test.target.bed",
        log:
            "logs/test.target.log",
        params:
            extra = "--split" # optional
        wrapper:
            "v3.0.1/bio/cnvkit/target"

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
* ``annotate``: gene annotation databases, e.g. RefSeq or Ensembl, as a “flat” format (can be found at UCSC) (optional)

**Output:**

* ``bed``: bed file



Params
------

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




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", "")

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

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


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