Changes between Version 1 and Version 2 of net.sf.basedb.reggie/notes426


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Timestamp:
Apr 15, 2020, 11:26:19 AM (5 months ago)
Author:
Nicklas Nordborg
Comment:

Added instructions for new pipeline scripts and library preparation protocols

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  • net.sf.basedb.reggie/notes426

    v1 v2  
    33== A. Before updating Reggie ==
    44
    5 === 1. Install a new Picard version on the prime cluster ===
     5=== 1. Install new Picard version on the prime cluster ===
    66
    77We need Picard version 2.22.3 or higher since it fixes a problem with !NovaSeq data files and the !CheckIlluminaDirectory
    88function. Verify that the `<picard><path>` setting `reggie-config.xml` is poiting to the correct installation directory
    99and modify if needed. Picard can be downloaded from https://github.com/broadinstitute/picard/releases.
     10
     11=== 2. Install new/updated pipeline scripts ===
     12
     13There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk
     14Download and install at a suitable location on the prime cluster:
     15
     16 * `novaseq_status.sh`: Used by auto-confirmation to check status of !NovaSeq sequencing.
     17 * `mips_functions.sh`: Used by MIPs alignment.
    1018
    1119== B. Update Reggie ==
     
    1927Upload the `CTG_SampleSheet.xlsx` file to the `/home/SCANB/Templates` directory in BASE.
    2028
    21 === 2. Import variant annotations ===
     29=== 2. Create/update library preparation protocol for external sequencing ===
     30
     31In the **Register external sequencing** wizard, a **Library preparation** protocol must be selected.
     32The wizard will list protocols that has been annotated with `LibPrepTarget=External`. Either create
     33a new protocol or add the External option to an existing protocol.
     34
     35=== 3. Import variant annotations ===
    2236
    2337In the **RNA library preparation and analysis**/**Variant calling pipeline** section,