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addressing @mestaki comments
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antgonza committed Jul 8, 2021
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9 changes: 8 additions & 1 deletion qiita_pet/static/js/networkVue.js
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Expand Up @@ -1147,7 +1147,14 @@ Vue.component('processing-graph', {
'<td rowspan="2">&nbsp;&nbsp;&nbsp;</td>' +
'<td rowspan="2" align="center">' +
'<a class="btn btn-success form-control" id="add-default-workflow"><span class="glyphicon glyphicon-flash"></span> Add Default Workflow</a>' +
"<br/><a href='https://qiita.ucsd.edu/workflows/' target='_blank'>What's a Default Workflow?</a>" +
"<br/><br/><a href='https://qiita.ucsd.edu/workflows/' target='_blank'> "+
'<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-exclamation-triangle" viewBox="0 0 16 16">' +
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'</svg>' +
" Important note about Default Workflow</a>" +
'</td>' +
'</tr>' +
'<tr>' +
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17 changes: 9 additions & 8 deletions qiita_pet/templates/workflows.html
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Expand Up @@ -68,16 +68,17 @@ <h3>Recommended Default Workflows</h3>
<div class="col-sm-10">
In this page you will find our recommendations on how to processes each data type available in Qiita and the minimum processing requirements to make your data public.
<br/><br/>
For convenience, there is a "Add Default Workflow" button on each preparation, that will allow you to add all this steps to
your raw data; however, all data is different and some of these steps will not work with it so we recommend checking that at least
the initial steps work for your data. An example of this, for target gene we assume you are uploading raw multiplexed EMP data with
reversed barcodes in your mapping file and index sequence file (EMP default). If that specific step doesn't apply to your data, you
can add and run whatever processing steps makes the most sense to your data and then add the rest of the steps by using that button.
For convenience, there is an "Add Default Workflow" button for each preparation that will add the recommended workflow steps for your raw data which then you can process.
It is important to note however that some steps it this default workflow will not work with all raw data; for example, for target gene the workflow is based on the
default Earth Microbiome Project protocol and so assumes the uploaded data are multiplexed sequences with the reversed barcodes in your mapping file and index sequence
file (<a href="https://earthmicrobiome.org/protocols-and-standards/" target="_blank">see here</a> for more details). Thus, if the protocol does not apply to your data
you can still use the Default Workflow, however, you should first manually process your data using the appropriate steps until you have a defined step; in our example,
demultiplexed your reads. After demultiplexing the Default Workflow is safe to use with any protocol.
<br/><br/>
By the way, if you have already performed one of the processes in this pipeline, the button "Add Default Workflow" will not re-run that step but instead will
run any other steps that havehas not been completed.
If you have already manually performed one of the processing steps in the Defaul Workflow pipeline, the "Add Default Workflow" button will not re-select those steps but
instead will only select any remaining steps that have not been completed. You can also add additional workflows on top of the recommended Default Workflow at any time.
<br/><br/>
Note that this is not a full inclusive list of data types accepted by Qiita but those that have a <u>defined</u> workflow.
Note that this is not a full inclusive list of data types accepted by Qiita but only those that have a defined workflow.
</div>
</div>
<h5>Hover on the spheres to get more information</h5>
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