.. _`bio/bwa/aln`:

BWA ALN
=======


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

Map reads with bwa aln. For more information about BWA see `BWA documentation <http://bio-bwa.sourceforge.net/bwa.shtml>`_.

**URL**: https://github.com/lh3/bwa

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bwa_aln:
        input:
            fastq="reads/{sample}.{pair}.fastq",
            idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
        output:
            "sai/{sample}.{pair}.sai",
        params:
            extra="",
        log:
            "logs/bwa_aln/{sample}.{pair}.log",
        threads: 8
        wrapper:
            "v3.0.1/bio/bwa/aln"

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 arguments for bwa-mem.
* The `sorting` param allows to enable sorting, and can be either 'none', 'samtools' or 'picard'.
* The `sort_extra` allows for extra arguments for samtools/picard


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

* ``bwa=0.7.17``

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

* fastq" FASTQ file(s)
* ``idx``: BWA reference genome index

**Output:**

* SAI file




Authors
-------

* Julian de Ruiter
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for bwa aln."""

    __author__ = "Julian de Ruiter"
    __copyright__ = "Copyright 2017, Julian de Ruiter"
    __email__ = "julianderuiter@gmail.com"
    __license__ = "MIT"

    from os import path
    from snakemake.shell import shell


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

    index = snakemake.input.idx
    if isinstance(index, str):
        index = path.splitext(snakemake.input.idx)[0]
    else:
        index = path.splitext(snakemake.input.idx[0])[0]

    shell(
        "bwa aln"
        " {extra}"
        " -t {snakemake.threads}"
        " {index}"
        " {snakemake.input.fastq}"
        " > {snakemake.output[0]} {log}"
    )


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