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(hopefully) GDPR-compliant privacy policy
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‎src/main/resources/static/css/main-20170616.css

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#format-json {
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display: none;
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}
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/**
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* Light email-obfuscation
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*/
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.obf-hide {
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display: none;
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}
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.obf-at::before {
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content: "@"
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}

‎src/main/resources/templates/about.html

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<div class="container">
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<div class="row">
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<div class="col-md-12" role="main" id="main">
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<section id="about">
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<h1>About</h1>
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<div style="position:relative;float:right;height:0;padding-bottom:30%;width:50%;margin-left:20px;">
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<iframe src="https://www.youtube-nocookie.com/embed/_yjhVTmvxLU?rel=0?ecver=2" style="position:absolute;width:100%;height:100%;left:0" allowfullscreen="true"></iframe>
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</div>
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<p>CWL Viewer is a richly featured web visualisation suite for workflows written in the
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<a href="http://www.commonwl.org/">Common Workflow Language</a> with an aim of facilitating sharing,
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<a href="https://www.commonwl.org/">Common Workflow Language</a> with an aim of facilitating sharing,
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understanding and discovery as well as encouraging best practices when writing workflows and their
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tooling.</p>
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<p>Cite as: <code><a href="https://doi.org/10.7490/f1000research.1114375.1">https://doi.org/10.7490/f1000research.1114375.1</a></code></p>
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<p>Technical Report: <a href="https://doi.org/10.5281/zenodo.848163">https://doi.org/10.5281/zenodo.848163</a></p>
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<p>A <a href="https://doi.org/10.5281/zenodo.823535">Technical Report for this project can be viewed here</a>.</p>
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<p>CWL Viewer also won the <a href="https://f1000research.com/">F1000Research</a> Best Poster Award at
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<p>CWL Viewer also won the <a href="https://f1000research.com/">F1000Research</a> Best Poster
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<a href="https://bioexcel.eu/poster-award-for-cwlviewer/"Award</a> at
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<a href="https://www.iscb.org/ismbeccb2017">ISMB/ECCB 2017</a> for its
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<a href="https://doi.org/10.7490/f1000research.1114375.1">poster submission.</a></p>
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<p>This project was developed at the <a href="http://www.esciencelab.org.uk/">eScience Lab</a> at
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<a href="http://www.manchester.ac.uk/">The University of Manchester</a>, with work supported by
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<a href="http://bioexcel.eu/">Bioexcel</a>, funded by the European Union Horizon 2020 program under
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<a href="http://cordis.europa.eu/projects/675728">grant agreement 675728.</a></p>
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<p>This project was developed at the <a href="https://www.esciencelab.org.uk/">eScience Lab</a> at
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<a href="https://www.manchester.ac.uk/">The University of Manchester</a>, with work supported by
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<a href="https://bioexcel.eu/">Bioexcel</a>, funded by the European Union Horizon 2020 program under
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<a href="https://cordis.europa.eu/projects/675728">grant agreement 675728.</a></p>
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<p>Contributions are welcome in the form of issues and pull requests to the
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<p>Contributions are welcome in the form of <em>issues</em> and
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<em>pull requests</em> to the
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<a href="https://github.com/common-workflow-language/cwlviewer">Github repository</a>.</p>
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</section>
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<section id="privacy">
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<h1>Privacy policy</h1>
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<p>CWL Viewer publish visualizations of workflows from publicly available
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<em>git</em> repositories hosted by third-parties like <a href="https://github.com/">GitHub</a>
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or <a href="https://about.gitlab.com/">GitLab</a>.
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Submitted workflows are added
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to our <a href="/workflows">public listing</a>.
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</p>
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<section id="track-use">
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<h2>Tracking usage</h2>
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<p>
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We do not track individual users of CWL Viewer, but we do record
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general usage (e.g. web server access log)
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for operational purposes and to prevent abuse.
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We may use HTTP session cookies in order to assist
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workflow submission, but do not use cookies to identify users.
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</section>
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</p>
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<section id="what-info">
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<h2>What information is held?</h2>
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<p>
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Metadata shown from the public workflows may include personal data,
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including authorship or as part of workflow descriptions.
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We retrieve this information from the submitted git repository.
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Downloading a workflow or its metadata may include
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information from the git repository not otherwise
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shown in the CWL Viewer interface, e.g. authors from git commit history.
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</p>
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<p>
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For performance reasons the CWL Viewer may keep a copy of the
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checked out git repository and the derived metadata.
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We may at a later date retrieve published changes
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from the original repository to update the information held.
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</p>
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</section>
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<section>
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<h2>Data controller</h2>
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<p>
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The <em>Data Controller</em> for the
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<a href="https://view.commonwl.org/">https://view.commonwl.org/</a> instance of CWL Viewer
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is The University of Manchester, contact
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<a href="javascript:window.location.href=atob('bWFpbHRvOmluZm9AZXNjaWVuY2VsYWIub3JnLnVr')"
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<code><span class="obf-hide">NOT</span>info<span class="obf-at"></span><span class="obf-hide">()</span><span class="obf-hide">NONE</span>esciencelab.org.uk</code></a> for any enquiries.
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If this viewer is accessed at a different URL, the data controller is likely someone else.
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</p>
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<p>
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<span class="obf-hide">(sorry non-css-non-JS folks, manual de-obfuscation needed above)</span>
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You may contact the Data Controller to request access to data about yourself,
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or to request update or removal of your personally identifiable information.
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You may also want to follow the <em>Shown Workflow</em> link at the bottom
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of any workflow page to locate the corresponding git repository from
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the original publisher.
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</p>
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</section>
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<section id="best-practice">
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<h1>Best Practices</h1>
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<p>In order to ensure that your workflow is well presented in CWL Viewer, we recommend the following of
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<a href="http://www.commonwl.org/user_guide/rec-practices/">CWL Best Practices</a>. Those which are
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specifically relevant to the viewer are detailed below, but it is suggested that you try to meet as
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many as possible to include the general quality and reproducibility of your workflows.</p>
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<p>Some limitations of the CWL Viewer which you may need to be aware of are also described here.</p>
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<section id="label">
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<h2>Label Strings</h2>
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<p class="recommendation">Include a top level short <code>label</code> summarising each tool and workflow</p>
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<p class="why">Labels give the user an easy human-readable version of the name for the tool or workflow</p>
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is given at the step level, it will take priority over the top level tool <code>label</code>. You can
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use this to provide a more descriptive label of the tool's application in the particular step if
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preferred.</p>
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</section>
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<h2>Doc Strings</h2>
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<section id="conceptual">
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<h2 id="doc">Doc Strings</h2>
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<p class="recommendation">If useful, include a top level <code>doc</code> string providing a longer, more detailed description
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than was provided in the <code>label</code> (see above)</p>
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<p class="why">Docs give the user a detailed description of the role a tool or workflow performs</p>
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<p class="use">For workflows this will be displayed at the top of the page under the title and for tools it will be
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displayed in the table. If a <code>doc</code> string is given at the step level, it will take priority
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over the top level tool doc. You can use this to provide a more descriptive label of the tool's
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application in the particular step if preferred</p>
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</section>
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<section id="conceptual">
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<h2>Conceptual Identifiers</h2>
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<p class="recommendation">All <code>input</code> and <code>output</code> identifiers should reflect their conceptual identity.
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Generic and uninformative names such as <code>result</code> or <code>input</code>/<code>output</code>
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should be avoided</p>
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<p class="why">Helpful identifiers allow for the links between steps in the CWL file to be easily distinguished</p>
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<p class="use">Identifiers are displayed in the tables and are unique to the step. The <code>label</code> is also
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used as a replacement for the identifier in the visualisation if provided.</p>
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</section>
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<section id="format">
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<h2>Format Specification</h2>
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<p class="recommendation">The <code>format</code> field should be specified for all input and output <code>File</code>s</p>
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<p class="recommendation_more">
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for compatibility in formatting of files</p>
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<p class="use">Ontologies will be parsed and the name of and link to the format displayed in the table on workflow
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pages. Plain formats will have the iana.org link given but will not display the name of the format.</p>
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</section>
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<section id="separation-of-concerns">
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<h2>Separation of Concerns</h2>
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<p class="recommendation">Each <code>CommandLineTool</code> description should focus on a single operation only, even if the
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(sub)command is capable of more.</p>
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<p class="why">This allows for easier reuse of the tool in other workflows and understanding as to it's purpose</p>
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<p class="use">In CWL Viewer this ensures that steps are clear in purpose within the workflow and generated visualisation</p>
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<h2>JavaScript Elimination</h2>
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<h2 id="javascript">JavaScript Elimination</h2>
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<p class="recommendation">Evaluate all use of JavaScript for possible elimination or replacement. For instance, for the
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manipulation of <code>File</code> names and paths, often one of the built in <code>File</code>
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properties such as <code>basename</code>, <code>nameroot</code>, <code>nameext</code> etc
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makes JavaScript expressions a last resort</p>
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<p class="use">CWL viewer does not take into account JavaScript expressions when extracting information about your
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workflows</p>
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</section>
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<section id="subworkflows">
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<h2>Use of Subworkflows</h2>
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<p class="recommendation">CWL implementations which also implement <code>SubworkflowFeatureRequirement</code> can support nesting
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workflows as a step within others. Complex workflows with individual components which can be abstracted
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them able to be understood more easily</p>
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<p class="use">Subworkflows are simplified in the visualisations and are linked as a different workflow in the
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<code>Step</code> tables on each workflow page</p>
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</section>
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<section id="attribution">
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<h2>Attribution</h2>
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<p class="recommendation">Include attribution information in your workflow and tool descriptions</p>
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<p class="recommendation_more">
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<p class="use">CWLViewer parses attribution information for inclusion in the Research Object Manifest from
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both the Git commit logs and from the CWL descriptions themselves when expressed in the
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<a href="http://schema.org/author">http://schema.org/author</a> format as above</p>
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</section>
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<section id="licensing">
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<h2>Licensing</h2>
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<p class="recommendation">Include a <a href="https://opensource.org/licenses">OSI approved open source license</a>
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in your workflow and tool descriptions</p>
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s:license: "https://www.apache.org/licenses/LICENSE-2.0"
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</pre>
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</p>
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<p class="why">A permissive open source license allows others to remix and use your tooling and workflows
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to prevent the community from repeating development effort, allowing everyone to benefit</p>
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<p class="use">CWL Viewer is designed to allow people to locate and make use of the workflows developed by
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others as well as to share and demonstrate work, and open source licenses promote this goal</p>
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</section>
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</section>
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<section id="limitations">
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<h1>Limitations</h1>
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<h2>Packed Workflows</h2>
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<p>In the Common Workflow Language, multiple files can be combined into a single one to create a
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self-contained document with all the components of a workflow. In the reference implementation
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this is done by using <code>cwltool --pack</code>.</p>
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<p>CWL Viewer treats each file as an independent workflow and although it can parse a workflow from the file,
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it is not possible to choose which and any nested workflows are not able to be viewed.
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(<a href="https://github.com/common-workflow-language/cwlviewer/issues/103">see Github issue</a>)</p>
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<h2>Research Objects</h2>
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<p>Research Objects are constructed from the containing directory of the workflow file. This means tooling
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external to the directory but used by the workflow will not be included
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(<a href="https://github.com/common-workflow-language/cwlviewer/issues/103">see Github issue</a>)</p>
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<p>We recommend that you keep all files in the containing folder for current use of CWL Viewer</p>
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<h2>SSH Cloning</h2>
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<h2 id="ssh">SSH Cloning</h2>
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<p>SSH URLs are not able to be cloned or used as submodules due to the need for SSH keys to be set up.</p>
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<p>We do not plan SSH support due to the impact on reproducibility from this being made a required
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step to download the workflow.</p>
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<h2>Others</h2>
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<h2 id="others">Others</h2>
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<p>Other limitations or unimplemented features can be viewed
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<a href="https://github.com/common-workflow-language/cwlviewer">on the Github issues page</a></p>
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</section>
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</div>
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</div>
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</div>

‎src/main/resources/templates/fragments/footer.html

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<hr />
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<div class="col-lg-12 muted text-center">
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<a href="https://github.com/common-workflow-language/cwlviewer" rel="noopener" target="_blank">CWL Viewer</a>
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&copy; 2016-2017 <a href="https://github.com/common-workflow-language/" rel="noopener" target="_blank">Common Workflow Language Project</a>
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&copy; 2016-2018 <a href="https://www.commonwl.org/" rel="noopener" target="_blank">Common Workflow Language Project</a>
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and <a href="https://github.com/orgs/common-workflow-language/people" rel="noopener" target="_blank">contributors</a>.
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Distributed under <a href="https://www.apache.org/licenses/LICENSE-2.0" rel="noopener" target="_blank">Apache License, version 2.0</a>
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(required <a href="https://github.com/common-workflow-language/cwlviewer/blob/master/NOTICE.md" rel="noopener" target="_blank">attribution notices</a>)
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(required <a href="https://github.com/common-workflow-language/cwlviewer/blob/master/NOTICE.md" rel="noopener" target="_blank">attribution notices</a>).
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<br />
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<span th:if="${workflow != null}">
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<a th:href="@{${workflow.retrievedFrom.getUrl(workflow.lastCommit)}}" href="#" rel="noopener" target="_blank">Shown workflow</a> has separate copyright and license.
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</div>
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<div class="row logos">
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<div class="col-lg-12 muted text-center">
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<a href="http://www.commonwl.org/" rel="noopener" target="_blank"><img src="/img/CWL-Logo-nofonts.svg"
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<a href="https://www.commonwl.org/" rel="noopener" target="_blank"><img src="/img/CWL-Logo-nofonts.svg"
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alt="Common Workflow Language"/></a>
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<a href="http://www.esciencelab.org.uk/" rel="noopener" target="_blank"><img src="/img/manchester.svg"
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<a href="https://www.esciencelab.org.uk/" rel="noopener" target="_blank"><img src="/img/manchester.svg"
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alt="The University of Manchester"
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title="eScienceLab, School of Computer Science, The University of Manchester" /></a>
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<a href="http://bioexcel.eu/" rel="noopener" target="_blank"><img src="/img/BioExcel_logo_cropped.svg"
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<a href="https://bioexcel.eu/" rel="noopener" target="_blank"><img src="/img/BioExcel_logo_cropped.svg"
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alt="BioExcel" title="BioExcel Center of Excellence for Computational Biomolecular Research" /></a>
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<a href="http://cordis.europa.eu/projects/675728" rel="noopener" target="_blank"><img src="/img/Flag_of_Europe.svg"
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<a href="https://cordis.europa.eu/projects/675728" rel="noopener" target="_blank"><img src="/img/Flag_of_Europe.svg"
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alt="EU" title="European Commision grant 675728" /></a>
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</div>
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</div>

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