.. _`bio/bwa/mem`:

BWA MEM
=======


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

Map reads using bwa mem, with optional sorting using samtools or picard.

**URL**: http://bio-bwa.sourceforge.net/bwa.shtml

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bwa_mem:
        input:
            reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
            idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
        output:
            "mapped/{sample}.bam",
        log:
            "logs/bwa_mem/{sample}.log",
        params:
            extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
            sorting="none",  # Can be 'none', 'samtools' or 'picard'.
            sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
            sort_extra="",  # Extra args for samtools/picard.
        threads: 8
        wrapper:
            "v3.0.1/bio/bwa/mem"

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``
* ``samtools=1.18``
* ``picard-slim=3.1.1``
* ``snakemake-wrapper-utils=0.6.2``

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

* FASTQ file(s)
* reference genome

**Output:**

* SAM/BAM/CRAM file




Authors
-------

* Johannes Köster
* Julian de Ruiter
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster, Julian de Ruiter"
    __copyright__ = "Copyright 2016, Johannes Köster and Julian de Ruiter"
    __email__ = "koester@jimmy.harvard.edu, julianderuiter@gmail.com"
    __license__ = "MIT"


    import tempfile
    from os import path
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts
    from snakemake_wrapper_utils.samtools import get_samtools_opts


    # Extract arguments.
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    sort = snakemake.params.get("sorting", "none")
    sort_order = snakemake.params.get("sort_order", "coordinate")
    sort_extra = snakemake.params.get("sort_extra", "")
    samtools_opts = get_samtools_opts(snakemake, param_name="sort_extra")
    java_opts = get_java_opts(snakemake)


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


    # Check inputs/arguments.
    if not isinstance(snakemake.input.reads, str) and len(snakemake.input.reads) not in {
        1,
        2,
    }:
        raise ValueError("input must have 1 (single-end) or 2 (paired-end) elements")


    if sort_order not in {"coordinate", "queryname"}:
        raise ValueError("Unexpected value for sort_order ({})".format(sort_order))


    # Determine which pipe command to use for converting to bam or sorting.
    if sort == "none":
        # Simply convert to bam using samtools view.
        pipe_cmd = "samtools view {samtools_opts}"

    elif sort == "samtools":
        # Add name flag if needed.
        if sort_order == "queryname":
            sort_extra += " -n"

        # Sort alignments using samtools sort.
        pipe_cmd = "samtools sort {samtools_opts} {sort_extra} -T {tmpdir}"

    elif sort == "picard":
        # Sort alignments using picard SortSam.
        pipe_cmd = "picard SortSam {java_opts} {sort_extra} --INPUT /dev/stdin --TMP_DIR {tmpdir} --SORT_ORDER {sort_order} --OUTPUT {snakemake.output[0]}"

    else:
        raise ValueError(f"Unexpected value for params.sort ({sort})")

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "(bwa mem"
            " -t {snakemake.threads}"
            " {extra}"
            " {index}"
            " {snakemake.input.reads}"
            " | " + pipe_cmd + ") {log}"
        )


.. |nl| raw:: html

   <br>