.. _`bio/vg/sim`:

VG SIM
======


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

Samples sequences from the xg-indexed graph.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule sim:
        input:
            xg="x.xg"
        output:
            reads="reads/x.seq"
        params:
            "--read-length 100 --num-reads 100 -f"
        log:
            "logs/vg/sim/x.log"
        threads:
            4
        wrapper:
            "v3.0.1/bio/vg/sim"

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 2018, Ali Ghaffaari"
    __email__ = "ghaffari@mpi-inf.mpg.de"
    __license__ = "MIT"


    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False)

    shell(
        "(vg sim {snakemake.params} --xg-name {snakemake.input.xg}"
        " --threads {snakemake.threads} > {snakemake.output.reads}) {log}"
    )


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