.. _`bio/bowtie2/build`:

BOWTIE2_BUILD
=============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bowtie2/build?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/bowtie2/build

Map reads with bowtie2.

**URL**: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bowtie2_build:
        input:
            ref="genome.fasta",
        output:
            multiext(
                "genome",
                ".1.bt2",
                ".2.bt2",
                ".3.bt2",
                ".4.bt2",
                ".rev.1.bt2",
                ".rev.2.bt2",
            ),
        log:
            "logs/bowtie2_build/build.log",
        params:
            extra="",  # optional parameters
        threads: 8
        wrapper:
            "v3.0.4/bio/bowtie2/build"



    rule bowtie2_build_large:
        input:
            ref="genome.fasta",
        output:
            multiext(
                "genome",
                ".1.bt2l",
                ".2.bt2l",
                ".3.bt2l",
                ".4.bt2l",
                ".rev.1.bt2l",
                ".rev.2.bt2l",
            ),
        log:
            "logs/bowtie2_build/build.log",
        params:
            extra="--large-index",  # optional parameters
        threads: 8
        wrapper:
            "v3.0.4/bio/bowtie2/build"

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.


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

* ``bowtie2=2.5.2``

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

* ``ref``: Path to FASTA reference

**Output:**

* Path to Bowtie2 reference index



Params
------

* ``extra``: additional program arguments besides `--threads` and io options.




Authors
-------

* Daniel Standage
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Daniel Standage"
    __copyright__ = "Copyright 2020, Daniel Standage"
    __email__ = "daniel.standage@nbacc.dhs.gov"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell

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


    index = os.path.commonprefix(snakemake.output).rstrip(".")


    shell(
        "bowtie2-build"
        " --threads {snakemake.threads}"
        " {extra}"
        " {snakemake.input.ref}"
        " {index}"
        " {log}"
    )


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