.. _`bio/minimap2/index`:

MINIMAP2 INDEX
==============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/minimap2/index?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/minimap2/index

creates a minimap2 index

**URL**: https://lh3.github.io/minimap2

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule minimap2_index:
        input:
            target="target/{input1}.fasta"
        output:
            "{input1}.mmi"
        log:
            "logs/minimap2_index/{input1}.log"
        params:
            extra=""  # optional additional args
        threads: 3
        wrapper:
            "v3.0.1/bio/minimap2/index"

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

* ``minimap2=2.26``

Input/Output
------------
**Input:**

* reference genome in FASTA format

**Output:**

* indexed reference genome




Authors
-------

* Tom Poorten


Code
----

.. code-block:: python

    __author__ = "Tom Poorten"
    __copyright__ = "Copyright 2017, Tom Poorten"
    __email__ = "tom.poorten@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    shell(
        "(minimap2 -t {snakemake.threads} {extra} "
        "-d {snakemake.output[0]} {snakemake.input.target}) {log}"
    )


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