.. _`bio/gridss/setupreference`:

GRIDSS SETUPREFERENCE
=====================


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

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. It includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. ``setupreference`` is a once-off setup generating additional files in the same directory as the reference. WARNING multiple instances of GRIDSS attempting to perform setupreference at the same time will result in file corruption. Make sure these files are generated before running parallel GRIDSS jobs.


**URL**: https://github.com/PapenfussLab/gridss

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gridss_setupreference:
        input:
            reference="reference/genome.fasta",
        output:
            idx=multiext("reference/genome.fasta", ".amb", ".ann", ".bwt", ".dict", ".fai", ".pac", ".sa")
        params:
            extra="--jvmheap 1g"
        log:
            "log/gridss/setupreference.log"
        wrapper:
            "v3.0.1/bio/gridss/setupreference"

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

* ``gridss=2.13.2``




Authors
-------

* Christopher Schröder


Code
----

.. code-block:: python

    """Snakemake wrapper for gridss setupreference"""

    __author__ = "Christopher Schröder"
    __copyright__ = "Copyright 2020, Christopher Schröder"
    __email__ = "christopher.schroede@tu-dortmund.de"
    __license__ = "MIT"

    from snakemake.shell import shell
    from os import path

    # Creating log
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")

    shell(
        "(gridss -s setupreference "  # Tool
        "--reference {snakemake.input.reference} "  # Reference
        "{extra}) {log}"
    )


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