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

Timestamp:

Apr 15, 2020, 11:26:19 AM (4 years ago)

Author:

Nicklas Nordborg

Comment:

Added instructions for new pipeline scripts and library preparation protocols

net.sf.basedb.reggie/notes426

@@ -3 +3 @@
 == A. Before updating Reggie ==
 
-=== 1. Install a new Picard version on the prime cluster ===
+=== 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 ==
@@ -19 +27 @@
 Upload the `CTG_SampleSheet.xlsx` file to the `/home/SCANB/Templates` directory in BASE.
 
-=== 2. Import variant annotations ===
+=== 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,