{% extends "!layout.html" %}

{% block sidebarsearch %}
    {{ super() }}
    <h3> Quick Reference:</h3>
    <ul>
        <ul>
            <li><a href="{{ pathto('faq') }}">FAQ</a>                                               </li>
            <li><a href="{{ pathto('history') }}">Changes</a>                                       </li>
            <li><a href="{{ pathto('todo') }}">Future plans</a>                                     </li>
        </ul>
        <h3><a href="{{ pathto('decorators/decorators') }}">Decorators:</a></h3>   
        <ul>
            <li><a href="{{ pathto('decorators/follows') }}">@follows / mkdir</a>                       </li>
            <li><a href="{{ pathto('decorators/files') }}">@files</a>                                   </li>
            <li><a href="{{ pathto('decorators/split') }}">@split</a>                                   </li>
            <li><a href="{{ pathto('decorators/transform') }}">@transform</a>                           </li>
            <li><a href="{{ pathto('decorators/merge') }}">@merge</a>                                   </li>
            <li><a href="{{ pathto('decorators/posttask') }}">@posttask touch_file</a>                  </li>
            <li><a href="{{ pathto('decorators/jobs_limit') }}">@jobs_limit</a>                         </li>
            <li><a href="{{ pathto('decorators/split_ex') }}">@split (regex / add_inputs)</a>             </li>
            <li><a href="{{ pathto('decorators/transform_ex') }}">@transform (add_inputs) </a>          </li>
            <li><a href="{{ pathto('decorators/collate') }}">@collate</a>                               </li>
            <li><a href="{{ pathto('decorators/collate_ex') }}">@collate (add_inputs)        </a>       </li>
            <li><a href="{{ pathto('decorators/jobs_limit') }}">@jobs_limit</a>                         </li>
            <li><a href="{{ pathto('decorators/files_ex') }}">@files (on the fly)</a>                   </li>
            <li><a href="{{ pathto('decorators/parallel') }}">@parallel</a>                             </li>
            <li><a href="{{ pathto('decorators/check_if_uptodate') }}">@check_if_uptodate</a>           </li>
        </ul>
    
        <h4 ><a href="{{ pathto('decorators/indicator_objects') }}">Indicator objects</a></h4>
        <h4 >Pipeline functions</h4>
        <ul>
            <li><a href="{{ pathto('pipeline_functions') }}#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
            <li><a href="{{ pathto('pipeline_functions') }}#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
            <li><a href="{{ pathto('pipeline_functions') }}#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
        </ul>
    </ul>
{% endblock %}

{% block rootrellink %}
        Ruffus v. {{ release }}
            <li><a href="{{ pathto('index') }}">Home</a> | </li>
            <li><a href="{{ pathto('contents') }}">Contents</a> | </li>
            <li><a href="{{ pathto('installation') }}">Install</a>  | </li>
            <li><a href="{{ pathto('tutorials/simple_tutorial/simple_tutorial') }}">Tutorial</a>  / </li>
            <li><a href="{{ pathto('tutorials/manual/manual_introduction') }}">Manual</a>  / </li>
            <li><a href="{{ pathto('examples/bioinformatics/index') }}">Bioinformatics</a>  | </li>
            <li><a href="{{ pathto('cheatsheet') }}">Cheat sheet</a> | </li>
            <li><a href="{{ pathto('python_template') }}">Python Template</a> | </li>
            <li><a href="{{ pathto('gallery') }}">Gallery</a>  &raquo;</li>
{% endblock %}




