.. _`bio/bwa-mem2/index`:

BWA-MEM2 INDEX
==============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bwa-mem2/index?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/bwa-mem2/index

Creates a bwa-mem2 index.

**URL**: https://github.com/bwa-mem2/bwa-mem2

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bwa_mem2_index:
        input:
            "{genome}",
        output:
            "{genome}.0123",
            "{genome}.amb",
            "{genome}.ann",
            "{genome}.bwt.2bit.64",
            "{genome}.pac",
        log:
            "logs/bwa-mem2_index/{genome}.log",
        wrapper:
            "v3.0.1/bio/bwa-mem2/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
---------------------

* ``bwa-mem2=2.2.1``

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

* Reference genome (FASTA )

**Output:**

* Indexed reference genome




Authors
-------

* Christopher Schröder
* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Christopher Schröder, Patrik Smeds"
    __copyright__ = "Copyright 2020, Christopher Schröder, Patrik Smeds"
    __email__ = "christopher.schroeder@tu-dortmund.de, patrik.smeds@gmail.com"
    __license__ = "MIT"

    from os import path
    from snakemake.shell import shell

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

    # Check inputs/arguments.
    if len(snakemake.input) == 0:
        raise ValueError("A reference genome has to be provided.")
    elif len(snakemake.input) > 1:
        raise ValueError("Please provide exactly one reference genome as input.")

    valid_suffixes = {".0123", ".amb", ".ann", ".bwt.2bit.64", ".pac"}


    def get_valid_suffix(path):
        for suffix in valid_suffixes:
            if path.endswith(suffix):
                return suffix


    prefixes = set()
    for s in snakemake.output:
        suffix = get_valid_suffix(s)
        if suffix is None:
            raise ValueError(f"{s} cannot be generated by bwa-mem2 index (invalid suffix).")
        prefixes.add(s[: -len(suffix)])

    if len(prefixes) != 1:
        raise ValueError("Output files must share common prefix up to their file endings.")
    (prefix,) = prefixes

    shell("bwa-mem2 index -p {prefix} {snakemake.input[0]} {log}")


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