.. _`bio/star/index`:

STAR INDEX
==========


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

Index fasta sequences with STAR

**URL**: https://github.com/alexdobin/STAR

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule star_index:
        input:
            fasta="{genome}.fasta",
        output:
            directory("{genome}"),
        message:
            "Testing STAR index"
        threads: 1
        params:
            extra="",
        log:
            "logs/star_index_{genome}.log",
        wrapper:
            "v3.0.1/bio/star/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
---------------------

* ``star=2.7.11a``

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

* A (multi)fasta formatted file

**Output:**

* A directory containing the indexed sequence for downstream STAR mapping



Params
------

* ``sjdbOverhang``: length of the donor/acceptor sequence on each side of the junctions (optional)

* ``extra``: additional program arguments.




Authors
-------

* Thibault Dayris
* Tomás Di Domenico
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for STAR index"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2019, Dayris Thibault"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    import tempfile
    from snakemake.shell import shell
    from snakemake.utils import makedirs

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

    sjdb_overhang = snakemake.params.get("sjdbOverhang", "")
    if sjdb_overhang:
        sjdb_overhang = f"--sjdbOverhang {sjdb_overhang}"

    gtf = snakemake.input.get("gtf", "")
    if gtf:
        gtf = f"--sjdbGTFfile {gtf}"


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "STAR"
            " --runThreadN {snakemake.threads}"  # Number of threads
            " --runMode genomeGenerate"  # Indexation mode
            " --genomeFastaFiles {snakemake.input.fasta}"  # Path to fasta files
            " {sjdb_overhang}"  # Read-len - 1
            " {gtf}"  # Highly recommended GTF
            " {extra}"  # Optional parameters
            " --outTmpDir {tmpdir}/STARtmp"  # Temp dir
            " --genomeDir {snakemake.output}"  # Path to output
            " {log}"  # Logging
        )


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