Updating to Reggie 4.26

A. Before updating Reggie

1. Install new Picard version on the prime cluster

We need Picard version 2.22.3 or higher since it fixes a problem with NovaSeq data files and the CheckIlluminaDirectory function. Verify that the <picard><path> setting reggie-config.xml is poiting to the correct installation directory and modify if needed. Picard can be downloaded from ​https://github.com/broadinstitute/picard/releases.

2. Install new/updated pipeline scripts

There are new pipeline scripts: ​http://baseplugins.thep.lu.se/browser/other/pipeline/trunk Download and install at a suitable location on the prime cluster:

• novaseq_status.sh: Used by auto-confirmation to check status of NovaSeq sequencing.
• mips_functions.sh: Used by MIPs alignment.

B. Update Reggie

Update Reggie to version 4.26 as usual. Do not forget to run the Installation wizard.

C. After updating Reggie

1. Upload CTG sample sheet template

Upload the CTG_SampleSheet.xlsx file to the /home/SCANB/Templates directory in BASE.

2. Create/update library preparation protocol for external sequencing

In the Register external sequencing wizard, a Library preparation protocol must be selected. The wizard will list protocols that has been annotated with LibPrepTarget=External. Either create a new protocol or add the External option to an existing protocol.

3. Import variant annotations

In the RNA library preparation and analysis/Variant calling pipeline section, run the Import variants for existing variant call raw bioassays wizard. This wizard will import variants that are found in some interesting genes as annotations to existing raw bioassay items and will take several minutes to run. The same functionality is included in the regular variant calling script so the wizard is not needed in the future. See #1229 for more information.