Error in mRNA-seq allelic-mapping when using custom genome

[caballero]

Running the mRNA-seq in allelic-mapping mode when a custom reference genome is passed a YAML file (not being a registered genome by snakePipes) has issues because, during the diploid genome generation, it adds the full path to the YAML file to the expected files, causing errors for missing files.

This is not happening when a genome is passed by the id (i.e. dm6) this is not a problem as files just added the label to the files.

Possible solutions:

• if the genome is a path to a YAML file, obtain the basename and remove '.yaml' to be used as id

[katsikora]

I believe that this should now be fixed, but I'd add a CI test.