.. _`bio/kallisto/index`:

KALLISTO INDEX
==============


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

Index a transcriptome using kallisto.

**URL**: https://github.com/pachterlab/kallisto

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule kallisto_index:
        input:
            fasta="{transcriptome}.fasta",
        output:
            index="{transcriptome}.idx",
        params:
            extra="",  # optional parameters
        log:
            "logs/kallisto_index_{transcriptome}.log",
        threads: 1
        wrapper:
            "v3.0.4/bio/kallisto/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
---------------------

* ``kallisto=0.50.1``

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

* ``fasta``: FASTA file to index

**Output:**

* ``index``: indexed file



Params
------

* ``extra``: Additional parameters




Authors
-------

* Joël Simoneau


Code
----

.. code-block:: python

    """Snakemake wrapper for Kallisto index"""

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

    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 is required"
    fasta = " ".join(fasta) if isinstance(fasta, list) else fasta

    shell(
        "kallisto index"  # Tool
        " --threads {snakemake.threads}"
        " {extra}"  # Optional parameters
        " --index {snakemake.output.index}"  # Output file
        " {fasta}"  # Input FASTA files
        " {log}"  # Logging
    )


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