.. _`bio/rebaler`:

REBALER
=======


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

Reference-based long read assemblies of bacterial genomes


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule rebaler:
        input:
            reference="ref.fa",
            reads="{sample}.fq",
        output:
            assembly="{sample}.asm.fa",
        log:
            "logs/rebaler/{sample}.log",
        params:
            extra="",
        wrapper:
            "v3.0.1/bio/rebaler"

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

* ``rebaler=0.2.0``




Authors
-------

* Michael Hall


Code
----

.. code-block:: python

    """Snakemake wrapper for Rebaler - https://github.com/rrwick/Rebaler"""

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2020, Michael Hall"
    __email__ = "michael@mbh.sh"
    __license__ = "MIT"

    from snakemake.shell import shell


    def get_named_input(name):
        value = snakemake.input.get(name)
        if value is None:
            raise NameError("Missing input named '{}'".format(name))
        return value


    def get_named_output(name):
        return snakemake.output.get(name, snakemake.output[0])


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

    reference = get_named_input("reference")
    reads = get_named_input("reads")
    output = get_named_output("assembly")

    shell("rebaler {extra} -t {snakemake.threads} {reference} {reads} > {output} {log}")


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