.. _`cutadapt`:

Cutadapt
==========

Trim single-end or paired-end reads using cutadapt.


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


* cutadapt >=1.16


Example
-------

.. code-block:: bash

  rule cutadapt:
    input:
      "raw/{sample}_R1.fastq.gz", "raw/{sample}_R2.fastq.gz" # Up to two (paired-end) fastq files.
    output:
      fastq1 = "trimmed/{sample}_R1.fastq.gz", # The output file of the first mate.
      fastq2 = "trimmed/{sample}_R2.fastq.gz", # (optional) The output file of the second mate.
      qc = "stats/{sample}.qc" # A text file containing trimming statistics
    params:
      options = "" # Additional command line options.
    wrapper:
      "cutadapt"


Usage
-----

Run snakemake with

.. code-block:: bash

  snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper ``cutadapt`` and include it in the snakefile.

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.




Authors
-------


* Julian de Ruiter

* Jens Preussner