For $vertrna (string 'embl_vertrna-[0-9]'), substitute '[' for '\[' and also ']' for '\]' (to get string 'embl_vertrna-\[0-9\]') and pass this to store_unmapped_cdnas.pl instead of the original string. This is necessary because GetOpt::Long does not parse the original string as expected.
For $vertrna (string 'embl_vertrna-[0-9]'), substitute '[' for '\[' and also ']' for '\]' (to get string 'embl_vertrna-\[0-9\]') and pass this to store_unmapped_cdnas.pl instead of the original string. This is necessary because GetOpt::Long does not parse the original string as expected.

Ensembl/ensembl-pipeline,Ensembl/ensembl-pipeline,Ensembl/ensembl-pipeline