.. _`bio/sickle/pe`:

SICKLE PE
=========


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

Trim paired-end reads with sickle.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule sickle_pe:
      input:
        r1="reads/{sample}.1.fastq",
        r2="reads/{sample}.2.fastq"
      output:
        r1="{sample}.1.fastq",
        r2="{sample}.2.fastq",
        rs="{sample}.single.fastq",
      log:
        "logs/sickle/{sample}.log"
      params:
        qual_type="sanger",
        # optional extra parameters
        extra=""
      wrapper:
        "v3.0.4/bio/sickle/pe"

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

* ``sickle-trim=1.33``




Authors
-------

* Wibowo Arindrarto


Code
----

.. code-block:: python

    __author__ = "Wibowo Arindrarto"
    __copyright__ = "Copyright 2016, Wibowo Arindrarto"
    __email__ = "bow@bow.web.id"
    __license__ = "BSD"

    from snakemake.shell import shell

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell()

    shell(
        "(sickle pe -f {snakemake.input.r1} -r {snakemake.input.r2} "
        "-o {snakemake.output.r1} -p {snakemake.output.r2} "
        "-s {snakemake.output.rs} -t {snakemake.params.qual_type} "
        "{extra}) {log}"
    )


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