.. _`bio/bustools/sort`:

BUSTOOLS SORT
=============


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

Sort raw BUS output from pseudoalignment programs

**URL**: https://github.com/BUStools/bustools#sort

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_bustools_sort:
        input:
            "file.bus",
        output:
            "sorted.bus",
        threads: 1
        resources:
            mem_mb=765,
        params:
            extra="--umi",
        log:
            "bustools.log",
        wrapper:
            "v3.0.1/bio/bustools/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
-----

`--temp` is automatically defined through `resources.tmpdir`

`--memory` is automatically defined through `resources.mem_mb`

Multiple bus files in input will result in a single bus file in output.

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

* ``bustools=0.43.1``
* ``snakemake-wrapper-utils=0.6.2``

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

* Path to bus file, or list of bus files

**Output:**

* Path to bus file



Params
------

* ``extra``: Optional parameters




Authors
-------



Code
----

.. code-block:: python

    #!/usr/bin/env python3
    # coding: utf-8

    """Snakemake wrapper for bustools sort"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2022, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell
    from tempfile import TemporaryDirectory
    from snakemake_wrapper_utils.snakemake import get_mem

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

    bus_files = snakemake.input
    if isinstance(bus_files, list):
        bus_files = " ".join(bus_files)

    mem = get_mem(snakemake, "MiB")


    with TemporaryDirectory() as tempdir:
        shell(
            "bustools sort "
            "--memory {mem} "
            "--temp {tempdir} "
            "--threads {snakemake.threads} "
            "--output {snakemake.output[0]} "
            "{bus_files} "
            "{log}"
        )


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