Changeset 2021


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

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).

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
1 added
4 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/META-INF/extensions.xml

    r2019 r2021  
    7676    </about>
    7777    <plugin-class>net.sf.basedb.reggie.plugins.QubitSampleNameExporter</plugin-class>
     78    <settings>
     79      <property name="everyone-use">1</property>
     80      <property name="immediate-execution">1</property>
     81    </settings>
     82  </plugin-definition>
     83
     84  <plugin-definition id="FlowCellSampleSheetExporter">
     85    <about>
     86      <name>Flow cell sample sheet exporter</name>
     87      <description>
     88        Plug-in for exporting information about libraries used in a flow cell.
     89        The generated tab-separated text file used used by analysis software
     90        to pick up data from the sequencing.
     91      </description>
     92    </about>
     93    <plugin-class>net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter</plugin-class>
    7894    <settings>
    7995      <property name="everyone-use">1</property>
  • 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.
     142
     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
     147
     148A number means repeat the preceding letter this many times.
     149
     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>
    128169</configfile>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

    r2020 r2021  
    520520  public static final Annotationtype POOL_MOLARITY =
    521521    new Annotationtype("PoolMolarity", Type.FLOAT, Item.EXTRACT);
    522  
     522
     523  /**
     524    The "FlowCellID" annotation, used for physical bioassays (FlowCell).
     525    @since 2.13
     526  */
     527  public static final Annotationtype FLOWCELL_ID =
     528    new Annotationtype("FlowCellID", Type.STRING, Item.PHYSICALBIOASSAY);
     529
    523530 
    524531  /**
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r2020 r2021  
    6161import net.sf.basedb.reggie.plugins.CaliperRunParametersExporter;
    6262import net.sf.basedb.reggie.plugins.CaliperSampleNameExporter;
     63import net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter;
    6364import net.sf.basedb.reggie.plugins.QubitSampleNameExporter;
    6465import net.sf.basedb.util.EqualsHelper;
     
    274275        jsonChecks.add(checkAnnotationType(dc, Annotationtype.AMPLIFICATION_OPERATOR, 1, null, effectiveOptions, createIfMissing));
    275276
     277        jsonChecks.add(checkAnnotationType(dc, Annotationtype.FLOWCELL_ID, 1, null, effectiveOptions, createIfMissing));
     278       
    276279        // Annotation type categories
    277280        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.PATIENT, createIfMissing,
     
    347350            Annotationtype.POOL_MOLARITY, Annotationtype.POOL_CONC, Annotationtype.OPERATOR));
    348351
     352        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FLOW_CELL, createIfMissing,
     353            Annotationtype.FLOWCELL_ID, Annotationtype.OPERATOR, Annotationtype.PLATE_PROCESS_RESULT));
     354       
    349355        // Plugin definitions and configurations
    350356        jsonChecks.add(checkPlugin(dc, CaliperSampleNameExporter.class, effectiveOptions, createIfMissing));
     
    352358        jsonChecks.add(checkPlugin(dc, CaliperLibPrepParametersExporter.class, effectiveOptions, createIfMissing));
    353359        jsonChecks.add(checkPlugin(dc, QubitSampleNameExporter.class, effectiveOptions, createIfMissing));
     360        jsonChecks.add(checkPlugin(dc, FlowCellSampleSheetExporter.class, effectiveOptions, createIfMissing));
     361       
    354362        jsonChecks.add(checkPluginConfiguration(dc, CaliperRunParametersExporter.class, "Standard sensitivity", effectiveOptions, createIfMissing));
    355363        jsonChecks.add(checkPluginConfiguration(dc, CaliperRunParametersExporter.class, "High sensitivity", effectiveOptions, createIfMissing));
    356364        jsonChecks.add(checkPluginConfiguration(dc, CaliperLibPrepParametersExporter.class, "HT DNA 1K Ver2 (96)", effectiveOptions, createIfMissing));
    357365        jsonChecks.add(checkPluginConfiguration(dc, CaliperLibPrepParametersExporter.class, "HT DNA 1K Ver2 (384)", effectiveOptions, createIfMissing));
    358        
     366
     367        jsonChecks.add(checkPluginConfiguration(dc, FlowCellSampleSheetExporter.class, "SCAN-B 2x50", effectiveOptions, createIfMissing));
     368
    359369        // Biomaterial lists
    360370        jsonChecks.add(checkBioMaterialList(dc, BiomaterialList.FLAGGED_RNA, createIfMissing));
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