.. _`bio/bwa/index`:

BWA INDEX
=========


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

Creates a BWA index.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bwa_index:
        input:
            "{genome}.fasta",
        output:
            idx=multiext("{genome}.{alg}", ".amb", ".ann", ".bwt", ".pac", ".sa"),
        log:
            "logs/bwa_index/{genome}.{alg}.log",
        params:
            extra=lambda w: f"-a {w.alg}",
        wrapper:
            "v3.0.1/bio/bwa/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.


Notes
-----

* Wrapper automatically calculates `block_size`.


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

* ``bwa=0.7.17``

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

* fasta file

**Output:**

* BWA index files



Params
------

* ``extra``: aditional program arguments




Authors
-------

* Patrik Smeds
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2016, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"

    from os.path import splitext
    from pathlib import Path
    from snakemake.shell import shell

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

    # Prefix that should be used for the database
    prefix = snakemake.params.get("prefix", splitext(snakemake.output[0])[0])

    # Block size should be a 10th of the reference length (https://github.com/lh3/bwa/issues/104)
    block_size = Path(snakemake.input[0]).stat().st_size / 1024 / 1024 / 10
    # If GZip, assume a 4-fold compression rate:
    # - https://scfbm.biomedcentral.com/articles/10.1186/s13029-019-0073-5/tables/3
    # - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336184/
    # - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866555/bin/supp_btt594_supplement-rev2.pdf
    # - https://softpanorama.org/HPC/DNA_sequencing/Genomic_data_compression/index.shtml
    if snakemake.input[0].endswith(".gz"):
        block_size *= 4

    # Ensure minimum (10 Mb as BWA default) and maximum (50Gb since no apparent gain and to limit memory usage) block size
    block_size = min(50 * 1024, max(10, int(block_size)))

    shell("bwa index -b {block_size}M -p {prefix} {extra} {snakemake.input} {log}")


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