.. _`reaper`:

Reaper
==========

Tool for demultiplexing, trimming and filtering sequencing data.


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


* reaper >=16.098


Example
-------

.. code-block:: bash

  rule reaper:
    input:
      "raw/{sample}.fastq" # Path to a (possibly gzipped) fastq file.
    output:
      "trimmed/{sample}.fastq.gz" # Path to the output file.
    params:
      options = "" # Additional command line options.
    wrapper:
      "reaper"


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 ``reaper`` 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
-------


* Jens Preussner