.. _`bio/razers3`:

RAZERS3
=======


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/razers3?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/razers3

Mapping (short) reads against a reference sequence. Can have multiple output formats, please see https://github.com/seqan/seqan/tree/master/apps/razers3


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule razers3:
        input:
            # list of input reads
            reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
        output:
            # output format is automatically inferred from file extension. Can be bam/sam or other formats.
            "mapped/{sample}.bam"
        log:
            "logs/razers3/{sample}.log"
        params:
            # the reference genome
            genome="genome.fasta",
            # additional parameters
            extra=""
        threads: 8
        wrapper:
            "v3.0.1/bio/razers3"

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

* ``razers3=3.5.8``




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2020, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    shell(
        "(razers3"
        " -tc {snakemake.threads}"
        " {extra}"
        " -o {snakemake.output[0]}"
        " {snakemake.params.genome}"
        " {snakemake.input.reads})"
        " {log}"
    )


.. |nl| raw:: html

   <br>