.. _`bio/cutadapt/pe`:

CUTADAPT-PE
===========


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

Trim paired-end reads using cutadapt.


**URL**: https://github.com/marcelm/cutadapt

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cutadapt:
        input:
            ["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
        output:
            fastq1="trimmed/{sample}.1.fastq",
            fastq2="trimmed/{sample}.2.fastq",
            qc="trimmed/{sample}.qc.txt",
        params:
            # https://cutadapt.readthedocs.io/en/stable/guide.html#adapter-types
            adapters="-a AGAGCACACGTCTGAACTCCAGTCAC -g AGATCGGAAGAGCACACGT -A AGAGCACACGTCTGAACTCCAGTCAC -G AGATCGGAAGAGCACACGT",
            # https://cutadapt.readthedocs.io/en/stable/guide.html#
            extra="--minimum-length 1 -q 20",
        log:
            "logs/cutadapt/{sample}.log",
        threads: 4  # set desired number of threads here
        wrapper:
            "v3.0.1/bio/cutadapt/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.


Notes
-----

* The `extra` param allows for additional program arguments.
* The `adapters` param allows for separatelly specifying adapter options (optional).


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

* ``cutadapt=4.5``

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

* two (paired-end) fastq files

**Output:**

* two trimmed (paired-end) fastq files
* text file containing trimming statistics




Authors
-------

* Julian de Ruiter
* David Laehnemann


Code
----

.. code-block:: python

    """Snakemake wrapper for trimming paired-end reads using cutadapt."""

    __author__ = "Julian de Ruiter"
    __copyright__ = "Copyright 2017, Julian de Ruiter"
    __email__ = "julianderuiter@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell


    n = len(snakemake.input)
    assert n == 2, "Input must contain 2 (paired-end) elements."

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

    assert (
        extra != "" or adapters != ""
    ), "No options provided to cutadapt. Please use 'params: adapters=' or 'params: extra='."

    shell(
        "cutadapt"
        " --cores {snakemake.threads}"
        " {adapters}"
        " {extra}"
        " -o {snakemake.output.fastq1}"
        " -p {snakemake.output.fastq2}"
        " {snakemake.input}"
        " > {snakemake.output.qc} {log}"
    )


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