Changeset 2581


Ignore:
Timestamp:
Aug 15, 2014, 1:19:26 PM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #547: Start Demux and Merge

Use different number of tiles when debugging for HiSeq? and NextSeq? data since one tile of HiSeq? data contains much more sequences and takes much longer time to process than one tile of NextSeq? data.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/reggie-ogs-hosts.xml

    r2566 r2581  
    7878      <!-- static options for the picard IlluminaBasecallsToFastq step -->
    7979      <fastq-options>ADAPTERS_TO_CHECK=null ADAPTERS_TO_CHECK=INDEXED ADAPTERS_TO_CHECK=PAIRED_END INCLUDE_NON_PF_READS=false MAX_READS_IN_RAM_PER_TILE=5000000 QUIET=true VERBOSITY=WARNING</fastq-options>
    80       <!-- number of tiles to process when debugging (default=16) -->
    81       <debug-tile-limit>16</debug-tile-limit>
     80      <!-- number of tiles to process when debugging (default=2 (HiSeq), 16 (NextSeq)) -->
     81      <debug-tile-limit-hiseq>2</debug-tile-limit-hiseq>
     82      <debug-tile-limit-nextseq>16</debug-tile-limit-nextseq>
    8283      <!-- static options for Trimmomatic -->
    8384      <trimmomatic-options>ILLUMINACLIP:${AdapterFile}:2:30:12:1:true LEADING:3 TRAILING:3 MAXINFO:40:0.9 MINLEN:20</trimmomatic-options>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java

    r2578 r2581  
    370370        String demux_extractOptions = cluster.getConfig("demux/extract-options", null);
    371371        String demux_fastqOptions = cluster.getConfig("demux/fastq-options", null);
    372         String debug_tileLimit = cluster.getConfig("demux/debug-tile-limit", "16");
     372        String debug_tileLimitHiSeq = cluster.getConfig("demux/debug-tile-limit-hiseq", "2");
     373        String debug_tileLimitNextSeq = cluster.getConfig("demux/debug-tile-limit-hiseq", "16");
    373374        String demux_trimmomaticOptions = cluster.getRequiredConfig("demux/trimmomatic-options");
    374375       
     
    587588            String flowCellBarcode = (String)Annotationtype.FLOWCELL_ID.getAnnotationValue(dc, flowCell);
    588589            Integer runNumber = (Integer)Annotationtype.SEQUENCING_RUN_NUMBER.getAnnotationValue(dc, seqRun);
     590            String flowCellType = (String)Annotationtype.FLOWCELL_TYPE.getAnnotationValue(dc, flowCell);
     591            String debug_tileLimit = "NextSeq".equals(flowCellType) ? debug_tileLimitNextSeq : debug_tileLimitHiSeq;
    589592            script.cmd("RUN_ARCHIVE=`find " + runArchive + " -maxdepth 2 -name " + dataFolder + " -type d -print -quit 2> /dev/null || true`");
    590593            script.cmd("if [ -z \"$RUN_ARCHIVE\" ]; then");
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