.. _`bio/sambamba/markdup`:

SAMBAMBA MARKDUP
================


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

Marks (default) or removes duplicate reads in BAM file. See details `here https://lomereiter.github.io/sambamba/docs/sambamba-markdup.html`_


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule sambamba_markdup:
        input:
            "mapped/{sample}.bam"
        output:
            "mapped/{sample}.rmdup.bam"
        params:
            extra="-r"  # optional parameters
        log:
            "logs/sambamba-markdup/{sample}.log"
        threads: 8
        wrapper:
            "v3.0.1/bio/sambamba/markdup"

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

* ``sambamba=1.0``

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

* bam file

**Output:**

* deduplicated bam file




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2021, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell
    from tempfile import TemporaryDirectory

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    with TemporaryDirectory() as tempdir:
        shell(
            "sambamba markdup {snakemake.params.extra} --nthreads {snakemake.threads} "
            "--tmpdir {tempdir} {snakemake.input[0]} {snakemake.output[0]} "
            "{log}"
        )


.. |nl| raw:: html

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