.. _`bio/meryl/count`:

MERYL COUNT
===========


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

A genomic k-mer counter (and sequence utility) with nice features.


**URL**: https://github.com/marbl/meryl

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule meryl_count:
        input:
            fasta="{genome}.fasta",
        output:
            directory("{genome}/"),
        log:
            "logs/meryl_count/{genome}.log",
        params:
            command="count",
            extra="k=32",
        threads: 2
        resources:
            mem_mb=2048,
        wrapper:
            "v3.0.4/bio/meryl/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.


Notes
-----

* The `command` param allows to specify how to count the kmers: `count` (canonical kmers) [default], `count-forward` (only forward kmers), or `count-reverse` (only reverse kmers).
* The `extra` param allows for additional program arguments (kmer size `k` is mandatory).


Software dependencies
---------------------

* ``meryl=2013``
* ``snakemake-wrapper-utils=0.6.2``

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

* fasta file

**Output:**

* meryl database




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    from snakemake.shell import shell
    from snakemake_wrapper_utils.snakemake import get_mem


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


    command = snakemake.params.get("command", "count")
    assert command in [
        "count",
        "count-forward",
        "count-reverse",
    ], "invalid command specified."


    mem_gb = get_mem(snakemake, out_unit="GiB")


    shell(
        "meryl"
        " {command}"
        " threads={snakemake.threads}"
        " memory={mem_gb}"
        " {extra}"
        " {snakemake.input}"
        " output {snakemake.output}"
        " {log}"
    )


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