.. _`bio/samtools/sort`:

SAMTOOLS SORT
=============


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

Sort bam file with samtools.

**URL**: http://www.htslib.org/doc/samtools-sort.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_sort:
        input:
            "mapped/{sample}.bam",
        output:
            "mapped/{sample}.sorted.bam",
        log:
            "{sample}.log",
        params:
            extra="-m 4G",
        threads: 8
        wrapper:
            "v3.0.1/bio/samtools/sort"

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

* ``samtools=1.18``
* ``snakemake-wrapper-utils=0.6.2``

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

* SAM/BAM/CRAM file

**Output:**

* SAM/BAM/CRAM file
* SAM/BAM/CRAM index file (optional)



Params
------

* ``extra``: additional program arguments (not `-@/--threads`, `--write-index`, `-m`, `-o` or `-O/--output-fmt`).




Authors
-------

* Johannes Köster
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2016, Johannes Köster"
    __email__ = "koester@jimmy.harvard.edu"
    __license__ = "MIT"


    import tempfile
    from pathlib import Path
    from snakemake.shell import shell
    from snakemake_wrapper_utils.snakemake import get_mem
    from snakemake_wrapper_utils.samtools import get_samtools_opts


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

    mem_per_thread_mb = int(get_mem(snakemake) / snakemake.threads)

    with tempfile.TemporaryDirectory() as tmpdir:
        tmp_prefix = Path(tmpdir) / "samtools_sort"

        shell(
            "samtools sort {samtools_opts} -m {mem_per_thread_mb}M {extra} -T {tmp_prefix} {snakemake.input[0]} {log}"
        )


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