.. _`bio/genomescope`:

GENOMESCOPE
===========


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

Reference-free profiling of polyploid genomes

**URL**: https://github.com/tbenavi1/genomescope2.0

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule genomescope:
        input:
            hist="{sample}.hist",
        output:
            multiext(
                "{sample}/",
                "linear_plot.png",
                "log_plot.png",
                "model.txt",
                "progress.txt",
                "SIMULATED_testing.tsv",
                "summary.txt",
                "transformed_linear_plot.png",
                "transformed_log_plot.png",
            ),
        log:
            "logs/genomescope/{sample}.log",
        params:
            extra="--kmer_length 32 --testing",
        wrapper:
            "v3.0.1/bio/genomescope"

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 `extra` param allows for additional program arguments (kmer length `-k`/`--kmer_length` is mandatory).


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

* ``genomescope2=2.0``

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

* kmer histogram

**Output:**

* inferred genome characteristics and plots




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell


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


    out_basename = os.path.commonpath(snakemake.output)


    shell("genomescope2 --input {snakemake.input} {extra} --output {out_basename} {log}")


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