Mar 18, 2020, 11:44:27 AM (22 months ago)
Nicklas Nordborg

References #1231: Add support for sequencing with NovaSeq?

Started to implement a wizard for registering a sample sheet from an external sequencing. A lot of checks are made to try to make sure that only the expected libraries are registered.

The wizard expects that library items have been pre-created and placed on a "External library plate" (it is not possible to do that by a wizard at the moment). The libraries should be without a 'creation date'.

The new wizard will set the 'creation date' to the date found in the sample sheet file (it is possible to manually change this), and associate the library with a barcode. Actual barcode sequences in the sample sheet are verified against the database.

The wizard will then create a single "Pooled library" item for all the libraries as well as a single "Flow cell" item and "Sequencing run". It will try to put in as much information as possible to make it possible for the "auto-confirmation" function to detect when data is available in the run archive and continue with demux and other analysis.

It should also be possible to use the manual "Sequencing ended" wizard.

At the moment, they doesn't work since some information is not yet available. We can probably parse out what we need from the "RunParameters?.xml" file, it just has to be done in a slightly different order.

1 edited


  • extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

    r5845 r5867  
    738738          <dt>
    739739            <base:icon image="<%=home+"/images/flowcell.png" %>" />
    740             Clustering and sequencing wizards
     740            Sequencing wizards
    741741          </dt>
    742742          <dd>
    763763            </ul>
    764764          </dd>
     766          <dt>
     767            <base:icon image="<%=home+"/images/lorry.png" %>" />
     768            External sequencing wizards
     769          </dt>
     770          <dd>
     771            <ul>
     773            <li><span class="require-permission" data-role="ExternalSequencing" data-link="sequencing/sequencing_external.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
     774              >Register external sequencing</span>
     775              <span class="counter" data-counter="external-libs-not-sequenced"
     776                title="Number of libraries sent for external sequencing">∙</span>
     777            </ul>
     778          </dd>
    766781          </dl>
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