.. _`bio/bcftools/sort`:

BCFTOOLS SORT
=============


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

Sort vcf/bcf file.

**URL**: http://www.htslib.org/doc/bcftools.html#sort

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcftools_sort:
        input:
            "{sample}.bcf",
        output:
            "{sample}.sorted.bcf",
        log:
            "logs/bcftools/sort/{sample}.log",
        params:
            # Set to True, in case you want uncompressed BCF output
            uncompressed_bcf=False,
            # Extra arguments
            extras="",
        resources:
            mem_mb=8000,
        wrapper:
            "v3.0.1/bio/bcftools/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.


Notes
-----

* The `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
* The `extra` param allows for additional program arguments (not `--threads`, `-o/--output`, `-O/--output-type`, `-m/--max-mem`, or `-T/--temp-dir`).


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

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




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2020, Filipe G. Vieira"
    __license__ = "MIT"


    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.bcftools import get_bcftools_opts


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


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "bcftools sort"
            " {bcftools_opts}"
            " {extra}"
            " --temp-dir {tmpdir}"
            " {snakemake.input[0]}"
            " {log}"
        )


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