.. _`bio/strling/index`:

STRLING INDEX
=============


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

STRling (pronounced like “sterling”) is a method to detect large short tandem repeat (STR) expansions from short-read sequencing data. ``index`` creates a bed file of large STR regions in the reference genome. This step is performed automatically as part of ``strling extract``. However, when running multiple samples, it is more efficient to do it once, then pass the file to strling extract using the ``-g`` option. Documentation at: https://strling.readthedocs.io/en/latest/run.html



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule strling_index:
        input:
            "reference/genome.fasta"
        output:
            index="reference/genome.fasta.str",
            fai="reference/genome.fasta.fai"
        params:
            extra="" # optionally add further command line arguments
        log:
            "log/strling/index.log"
        wrapper:
            "v3.0.1/bio/strling/index"

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

* ``strling=0.5.2``




Authors
-------

* Christopher Schröder


Code
----

.. code-block:: python

    """Snakemake wrapper for strling index"""

    __author__ = "Christopher Schröder"
    __copyright__ = "Copyright 2020, Christopher Schröder"
    __email__ = "christopher.schroede@tu-dortmund.de"
    __license__ = "MIT"

    from snakemake.shell import shell
    from os import path

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

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")

    # Check inputs/arguments.
    if len(snakemake.input) != 1:
        raise ValueError("Please provide exactly one reference genome.")

    shell(
        "(strling index {snakemake.input[0]} "
        "-g {snakemake.output.index} "
        "{extra}) {log}"
    )


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