.. _`bio/kallisto/quant`:

KALLISTO QUANT
==============


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

Pseudoalign reads and quantify transcripts using kallisto.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule kallisto_quant:
        input:
            fastq=["reads/{exp}_R1.fastq", "reads/{exp}_R2.fastq"],
            index="index/transcriptome.idx",
        output:
            directory("quant_results_{exp}"),
        params:
            extra="",
        log:
            "logs/kallisto_quant_{exp}.log",
        threads: 1
        wrapper:
            "v3.0.1/bio/kallisto/quant"

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=0.50.0``

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

* ``fastq``: FASTQ file(s)
* ``index``: indexed file

**Output:**

* directory with results



Params
------

* ``extra``: Additional parameters




Authors
-------

* Joël Simoneau


Code
----

.. code-block:: python

    """Snakemake wrapper for Kallisto quant"""

    __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 FASTQ files
    fastq = snakemake.input.get("fastq")
    assert fastq is not None, "input-> a FASTQ-file is required"
    fastq = " ".join(fastq) if isinstance(fastq, list) else fastq

    shell(
        "kallisto quant "  # Tool
        " --threads {snakemake.threads}"  # Number of threads
        " --index {snakemake.input.index}"  # Input file
        " {extra}"  # Optional parameters
        " --output-dir {snakemake.output}"  # Output directory
        " {fastq}"  # Input FASTQ files
        " {log}"  # Logging
    )


.. |nl| raw:: html

   <br>