Currently, we use underscores in the config.yaml when specifying a contrast (i.e Kisumu_Tiassale), but this means that underscores cannot be used in treatment names. It's not the end of the world, but this is probably quite a regular use case.
We could use lists i.e ['Kisumu', 'Tiassale'] instead. I would prefer to keep manual specification of contrasts as it allows for the most flexibility.
It would require some minor editing of almost every script in the workflow.
Currently, we use underscores in the config.yaml when specifying a contrast (i.e Kisumu_Tiassale), but this means that underscores cannot be used in treatment names. It's not the end of the world, but this is probably quite a regular use case.
We could use lists i.e ['Kisumu', 'Tiassale'] instead. I would prefer to keep manual specification of contrasts as it allows for the most flexibility.
It would require some minor editing of almost every script in the workflow.