Updating to Reggie 4.40

1. New array design

Create a new array design, hg38gencode41filtered for representing the new GTF that should be used by StringTie/2023.

• Make sure that the Set as project default checkbox is set.
• The Pipeline annotation of the new array design should be set to RNAseq/StringTie/2023. The annotation type must be enabled for the ARRAYDESIGN item type first (this is done by the Reggie installation wizard but it is better to prepare this before installing the new version).
• Upload the gencode.v41.primary_assembly.annotation.ucsc.filtered.gtf and link it to the new array design. Place the GTF in the /home/SCANB/GTF directory. BASE should report that the file contains 88838 features.

2. Create new software items for Hisat/2023 and StringTie/2023

New software items are needed for Masking, Alignment and Feature extraction subtypes. The new items should describe the new 2023 pipeline. Make sure that the Add as project default checkbox is selected and that the Replace existing default is not. Annotate the new items with the correct Pipeline annotation (eg. RNAseq/Hisat/2023 or RNAseq/Hisat/StringTie). Also set the AlignmentType and ExpressionType values.

Also set the the Pipeline annotation for existing software items, or they will not be found the the wizards.

3. New configuration for Reggie and the Job scheduler extension

The Job scheduler extesion version 1.7 need to be installed. Create a new entry in the opengrid-config.xml for accessing the Slurm-based cluster. The slurm-accounting-disabled flag should be set unless accounting has been enabled before this update.

Create a new <host> entry in reggie-config.xml that is linked to the new cluster definition. Fill the <host> entry with configuration settings that are needed for running the Hisat/2023 and StringTie/2023 analysis steps. The configuration file that ships with Reggie should have an example that is is more or less complete already.

4. Update Reggie to 4.40

5. Disable auto-processing for the Hisat/2023 pipeline

Until we know how stable the new pipeline is it better to manually start. To disable auto-processing set AutoProcessing=Disable for the item list named Hisat/2023 Pipeline. The StringTie/2023 Pipeline doens't have to be disabled.

6. Test the new pipeline

Fix problems if there are any.