.. _`bio/filtlong`:

FILTLONG
========


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

Quality filtering tool for long reads.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule filtlong:
        input:
            reads = "{sample}.fastq"
        output:
            "{sample}.filtered.fastq"
        params:
            extra=" --mean_q_weight 5.0",
            target_bases = 10
        log:
            "logs/filtlong/test/{sample}.log"
        wrapper:
            "v3.0.1/bio/filtlong"

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

* ``filtlong=0.2.1``




Authors
-------

* Michael Hall


Code
----

.. code-block:: python

    """Snakemake wrapper for filtlong."""

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2019, Michael Hall"
    __email__ = "michael@mbh.sh"
    __license__ = "MIT"


    from snakemake.shell import shell

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")
    target_bases = int(snakemake.params.get("target_bases", 0))
    if target_bases > 0:
        extra += " --target_bases {}".format(target_bases)

    # Formats the log redrection string
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    # Executed shell command
    shell("filtlong {extra}" " {snakemake.input.reads} > {snakemake.output} {log}")


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