.. _`bio/bismark/bismark_genome_preparation`:

BISMARK_GENOME_PREPARATION
==========================


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

Generate indexes for Bismark (see https://github.com/FelixKrueger/Bismark/blob/master/bismark_genome_preparation).



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    # For *.fa file
    rule bismark_genome_preparation_fa:
        input:
            "indexes/{genome}/{genome}.fa"
        output:
            directory("indexes/{genome}/Bisulfite_Genome")
        log:
            "logs/indexes/{genome}/Bisulfite_Genome.log"
        params:
            ""  # optional params string
        wrapper:
            "v3.0.4/bio/bismark/bismark_genome_preparation"

    # Fo *.fa.gz file:
    rule bismark_genome_preparation_fa_gz:
        input:
            "indexes/{genome}/{genome}.fa.gz"
        output:
            directory("indexes/{genome}/Bisulfite_Genome")
        log:
            "logs/indexes/{genome}/Bisulfite_Genome.log"
        params:
            extra=""  # optional params string
        wrapper:
            "v3.0.4/bio/bismark/bismark_genome_preparation"

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

* ``bowtie2=2.5.2``
* ``bismark=0.24.2``
* ``samtools=1.18``

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

* path to genome \*.fa (or \*.fasta, \*.fa.gz, \*.fasta.gz) file

**Output:**

* No ouptut, generates bismark indexes in parent directory of input file




Authors
-------

* Roman Cherniatchik


Code
----

.. code-block:: python

    """Snakemake wrapper for Bismark indexes preparing using bismark_genome_preparation."""
    # https://github.com/FelixKrueger/Bismark/blob/master/bismark_genome_preparation

    __author__ = "Roman Chernyatchik"
    __copyright__ = "Copyright (c) 2019 JetBrains"
    __email__ = "roman.chernyatchik@jetbrains.com"
    __license__ = "MIT"


    from os import path
    from snakemake.shell import shell

    input_dir = path.dirname(snakemake.input[0])

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

    shell("bismark_genome_preparation --verbose --bowtie2 {params_extra} {input_dir} {log}")


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