.. _`bio/msisensor/scan`:

MSISENSOR SCAN
==============


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

Scan homopolymers and microsatelites with MSIsensor


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_msisensor_scan:
        input:
            "genome.fasta"
        output:
            "microsat.list"
        message:
            "Testing MSISensor scan"
        threads:
            1
        params:
            extra = ""
        log:
            "logs/msisensor_scan.log"
        wrapper:
            "v3.0.1/bio/msisensor/scan"

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

* ``msisensor=0.5``

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

* A (multi)fasta formatted file

**Output:**

* A text file containing homopolymers and microsatelites




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    """Snakemake script for MSISensor Scan"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2020, Dayris Thibault"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    # Extra parameters default value is an empty string
    extra = snakemake.params.get("extra", "")

    shell(
        "msisensor scan "  # Tool and its sub-command
        "-d {snakemake.input} "  # Path to fasta file
        "-o {snakemake.output} "  # Path to output file
        "{extra} "  # Optional extra parameters
        "{log}"  # Logging behavior
    )


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