[bulkRNASeq] NF_RCP 2.0.0 - Custom genomes are limited to organisms found in reference_table

[bnovak32]

Describe the bug Custom genome support is limited to organisms found in the pre-defined reference_table

To Reproduce Steps to reproduce the behavior:

1. Run the NF_RCP 2.0.0 main workflow on a dataset with an organism not belonging to the reference_table

Expected behavior The workflow should use the provided reference_source, reference_version, reference_fasta, and reference_gtf to build the correct references.

Additional context

• Assay: bulkRNASeq
• Workflow: NF_RCP
• Workflow version: 2.0.0

[bnovak32]

Workaround Create a new reference table that lists the custom organism following the [pipeline description for generating GeneLab Reference Annotations