.. _`bio/tabix/index`:

TABIX INDEX
===========


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

Process given file with tabix (e.g., create index).

**URL**: https://www.htslib.org/doc/tabix.html#INDEXING_OPTIONS

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule tabix:
        input:
            "{prefix}.vcf.gz",
        output:
            "{prefix}.vcf.gz.tbi",
        log:
            "logs/tabix/{prefix}.log",
        params:
            # pass arguments to tabix (e.g. index a vcf)
            "-p vcf",
        wrapper:
            "v3.0.4/bio/tabix/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.


Notes
-----

* Specify tabix index params (e.g. `-p vcf`) through `params`.


Software dependencies
---------------------

* ``htslib=1.18``

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

* Bgzip compressed file (e.g. BED.gz, GFF.gz, or VCF.gz)

**Output:**

* Tabix index file




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2016, Johannes Köster"
    __email__ = "koester@jimmy.harvard.edu"
    __license__ = "MIT"


    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    shell("tabix {snakemake.params} {snakemake.input[0]} {log}")


.. |nl| raw:: html

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