Ignore:
Timestamp:
Feb 19, 2020, 9:25:09 AM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1218: Implement MIPs alignment

Added Trimmomatic steps to the script. Logging and error handling is not fully implemented yet.

File:
1 edited

Legend:

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  • extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

    r5826 r5827  
    325325        <parallel-environment>smp 8-16</parallel-environment>
    326326       
     327        <!-- Options for Trimmomatic -->
     328        <trimmomatic>
     329          <!-- Optional path to Trimmomatic, if not specified the default in the 'programs' section is used -->
     330          <path>/usr/local/packages/trimmomatic/0.39/trimmomatic.jar</path>
     331          <!-- The first step should filter Illumina adapters-->
     332          <step-1>ILLUMINACLIP:adapter.fa:3:12:7:1:true MINLEN:30</step-1>
     333          <!-- The second step is for all other filters -->
     334          <step-2>MAXINFO:30:0.25 MINLEN:30</step-2>
     335        </trimmomatic>
     336       
    327337      </align-mips>
    328338     
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