.. _`bio/wgsim`:

WGSIM
=====


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

Short read simulator.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule wgsim:
        input:
            ref="genome.fa"
        output:
            read1="reads/1.fq",
            read2="reads/2.fq"
        log:
            "logs/wgsim/sim.log"
        params:
            "-X 0 -R 0 -r 0.1 -h"
        wrapper:
            "v3.0.1/bio/wgsim"

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

* ``wgsim=1.0``




Authors
-------

* Ali Ghaffaari


Code
----

.. code-block:: python

    __author__ = "Ali Ghaffaari"
    __copyright__ = "Copyright 2018, Ali Ghaffaari"
    __email__ = "ali.ghaffaari@mpi-inf.mpg.de"
    __license__ = "MIT"


    from snakemake.shell import shell

    log = snakemake.log_fmt_shell()

    shell(
        "(wgsim {snakemake.params} {snakemake.input.ref}"
        " {snakemake.output.read1} {snakemake.output.read2}) {log}"
    )


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