.. _`bio/cnvkit/call`:

CNVKIT CALL
===========


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

Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer  copy number. 


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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cnvkit_call:
        input:
            segment="test.cns",
            vcf="test.vcf",
        output:
            segment="test.call.cns",
        log:
            "logs/test.call.cns.log",
        params:
            extra = "" # optional
        wrapper:
            "v3.0.1/bio/cnvkit/call"

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:**

* ``segments``: Copy ratios (.cnr or .cns)
* ``vcf``: VCF file name containing variants for calculation of b-allele frequencies

**Output:**

* ``segments``: Output table file name (CNR-like table of segments, .cns)



Params
------

* ``filter``: Merge segments flagged by the specified filter(s) with the adjacent segment(s), optional

* ``purity``: purity value of the tumor

* ``ploidy``: Ploidy of the sample cells.

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




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)

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

    purity = snakemake.params.get("purity", "")
    if purity:
        purity = f"--purity {purity}"

    ploidy = snakemake.params.get("ploidy", "")
    if ploidy:
        ploidy = f"--ploidy {ploidy}"

    filter = snakemake.params.get("filter", "")
    if filter:
        filter = "--filter {filter}"

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

    shell(
        "(cnvkit.py call {snakemake.input.segment} "
        "{vcf} "
        "-o {snakemake.output.segment} "
        "{purity} "
        "{ploidy} "
        "{filter} "
        "{extra}) "
        "{log}"
    )


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