.. _`bio/jellyfish/count`:

JELLYFISH_COUNT
===============


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

Count k-mers in a fastn file using jellyfish.

**URL**: https://github.com/gmarcais/Jellyfish

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule jellyfish_count:
        input:
            "{prefix}.fasta",
        output:
            "{prefix}.jf",
        log:
            "{prefix}.jf.log",
        params:
            kmer_length=21,
            size="1G",
            extra="--canonical",
        threads: 2
        wrapper:
            "v3.0.4/bio/jellyfish/count"

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
---------------------

* ``kmer-jellyfish=2.3.0``

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

* sequence FASTA file

**Output:**

* kmer count jf file




Authors
-------

* William Rowell


Code
----

.. code-block:: python

    __author__ = "William Rowell"
    __copyright__ = "Copyright 2020, William Rowell"
    __email__ = "wrowell@pacb.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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


    shell(
        """
        (jellyfish count \
            {extra} \
            --mer-len={snakemake.params.kmer_length} \
            --size={snakemake.params.size} \
            --threads={snakemake.threads} \
            --output={snakemake.output} \
            {snakemake.input}) {log}
        """
    )


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