.. _`multiqc`:

Multiqc
==========

Generate qc report using multiqc.



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


* multiqc ==1.2

* networkx <2.0


Example
-------

.. code-block:: bash

  rule multiqc:
    input:
      "fastqc/" # An input directory containing qc files
    output:
      "QC-report.html" # qc report (html)
    wrapper:
      "multiqc"


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 ``multiqc`` 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