nf-core
DSL2: Options for different adapters for ssDNA and dsDNA libraries within the same run.
ssDNA libraries have a different R2 adapter than dsDNA libraries, meaning that processing both types of libraries together currently requires an adapterlist to be provided.
Omission of the list leaves behind small proportion of adapter sequences in PE sequences ssDNA libraries. The proportion of adapters is still small enough that it might be missed by the end user.
To bring attention to this fact, and to make it easier to process both dsDNA and ssDNA libraries in one run, it would be good to add a second pair of parameters to specify forward and reverse adapter sequences for ssDNA libraries.
or do we swap to always requiring an adapterlist, and provide default adapters there? 🤔