.. _`fastqc`:

Fastqc
==========

Generate fastq qc statistics using fastqc.



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


* fontconfig ==2.12.1

* fastqc ==0.11.5


Example
-------

.. code-block:: bash

  rule fastqc:
    input:
      "raw/{sample.fastq}" # A fastq file
    output:
      html = "fastqc/{sample}.html", # HTML file containing statistics
      zip = "fastqc/{sample}.zip" # Zip file containing statistics
    wrapper:
      "fastqc"


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 ``fastqc`` 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