.. _`bio/bedtools/slop`:

SLOPBED
=======


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

Increase the size of each feature in a BED/BAM/VCF by a specified factor.

**URL**: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bedtools_merge:
        input:
            "A.bed"
        output:
            "A.slop.bed"
        params:
            ## Genome file, tab-seperated file defining the length of every contig
            genome="genome.txt",
            ## Add optional parameters
            extra = "-b 10" ## in this example, we want to increase the feature by 10 bases to both sides
        log:
            "logs/slop/A.log"
        wrapper:
            "v3.0.1/bio/bedtools/slop"

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
-----

* Extra parameters requires either `-b` or (`-l` and `-r`)
* This program/wrapper does not handle multi-threading.

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

* ``bedtools=2.31.1``

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

* Path to an interval file (BED/GFF/VCF)

**Output:**

* Path to the expanded intervals file



Params
------

* ``genome``: Path to a genome file

* ``extra``: additional program arguments (except for `-i` or `-g`)




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2019, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"

    from snakemake.shell import shell

    ## Extract arguments
    extra = snakemake.params.get("extra", "")

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

    shell(
        "(bedtools slop"
        " {extra}"
        " -i {snakemake.input[0]}"
        " -g {snakemake.params.genome}"
        " > {snakemake.output})"
        " {log}"
    )


.. |nl| raw:: html

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