Sep 17, 2013, 1:05:46 PM (8 years ago)
Nicklas Nordborg

References #499: Export sample sheet for flow cell

First implementation of an export plug-in. It is yet a bit uncertain were some information should be coming from. Eg. the ReadString? is now configuration parameter for the plug-in, but it may be better to store this as an annotation on the flow cell (as is done for 'operator' and 'flow cell id'). Some information is still hard-coded in the plug-in (eg. concentration = 12pM).

1 edited


  • extensions/net.sf.basedb.reggie/trunk/META-INF/plugin-configurations.xml

    r1901 r2021  
    126126    </parameter>
    127127  </configuration>
     128  <configuration pluginClassName="net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter">
     129    <configname>SCAN-B 2x50</configname>
     130    <description>Configuration for the default SCAN-B setup. Read string is Y54N1I6J1Y53N1.</description>
     131    <parameter>
     132      <name>SequencingCenter</name>
     133      <label>Sequencing center</label>
     134      <description>LuOnk</description>
     135      <class>java.lang.String</class>
     136      <value>LuBMC</value>
     137    </parameter>
     138    <parameter>
     139      <name>ReadString</name>
     140      <label>Read string</label>
     141      <description>Pattern describing how each sequencing cycle is used.
     143Y = the cycle should be used as part of an insert read
     144N = the cycle should be skipped
     145I = the cycle should be used as part of the index (barcode)
     146J = the cycle is part of the index but should not be used in demultiplexing
     148A number means repeat the preceding letter this many times.
     150The person responsible for the library should enter the requested pattern of sequencing cycles here. Checked and corrected by the operator who loads the libraries on the flowcell.</description>
     151      <class>java.lang.String</class>
     152      <value>Y54N1I6J1Y53N1</value>
     153    </parameter>
     154    <parameter>
     155      <name>Project</name>
     156      <label>Project</label>
     157      <description>Project name. Lower case letters (a-z), numbers and underscore are permitted. After sequencing is done, the sequence reads are converted to bam format and demultiplexed. One bam file is produced per lane and index. The bam files are deposited in separate folders for each project.</description>
     158      <class>java.lang.String</class>
     159      <value>scanb</value>
     160    </parameter>
     161    <parameter>
     162      <name>Width</name>
     163      <label>Width</label>
     164      <description>The width of the library size distribution at approximately 2/3 peak height.</description>
     165      <class>java.lang.Integer</class>
     166      <value>100</value>
     167    </parameter>
     168  </configuration>
Note: See TracChangeset for help on using the changeset viewer.