.. _`bio/vg/prune`:

VG PRUNE
========


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

Prunes the complex regions of the graph for GCSA2 indexing.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule prune:
        input:
            vg="c.vg"
        output:
            pruned="graph/c.pruned.vg"
        params:
            "-r"
        log:
            "logs/vg/prune/c.log"
        threads:
            4
        wrapper:
            "v3.0.1/bio/vg/prune"

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

* ``vg=1.52.0``




Authors
-------

* Ali Ghaffaari


Code
----

.. code-block:: python

    __author__ = "Ali Ghaffaari"
    __copyright__ = "Copyright 2017, Ali Ghaffaari"
    __email__ = "ghaffari@mpi-inf.mpg.de"
    __license__ = "MIT"


    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False)

    shell(
        "(vg prune --threads {snakemake.threads} {snakemake.params}"
        " {snakemake.input.vg} > {snakemake.output.pruned}) {log}"
    )


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