.. _`bio/hisat2/index`:

HISAT2 INDEX
============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/hisat2/index?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/hisat2/index

Create index with hisat2.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule hisat2_index:
        input:
            fasta = "{genome}.fasta"
        output:
            directory("index_{genome}")
        params:
            prefix = "index_{genome}/"
        log:
            "logs/hisat2_index_{genome}.log"
        threads: 2
        wrapper:
            "v3.0.1/bio/hisat2/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
---------------------

* ``hisat2=2.2.1``
* ``samtools=1.18``

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

* ``sequence``: list of FASTA files of list of sequences

**Output:**

* Directory of the hisat2 custom index.



Params
------

* ``prefix``: prefix of index file path (required). Must be related to output

* ``extra``: additional parameters




Authors
-------

* Joël Simoneau


Code
----

.. code-block:: python

    """Snakemake wrapper for HISAT2 index"""

    __author__ = "Joël Simoneau"
    __copyright__ = "Copyright 2019, Joël Simoneau"
    __email__ = "simoneaujoel@gmail.com"
    __license__ = "MIT"

    import os
    from snakemake.shell import shell

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

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

    # Allowing for multiple FASTA files
    fasta = snakemake.input.get("fasta")
    assert fasta is not None, "input-> a FASTA-file or a sequence is required"
    input_seq = ""
    if not "." in fasta:
        input_seq += "-c "
    input_seq += ",".join(fasta) if isinstance(fasta, list) else fasta

    hisat_dir = snakemake.params.get("prefix", "")
    if hisat_dir:
        os.makedirs(hisat_dir)

    shell(
        "hisat2-build {extra} "
        "-p {snakemake.threads} "
        "{input_seq} "
        "{snakemake.params.prefix} "
        "{log}"
    )


.. |nl| raw:: html

   <br>