Add choice to map all samples to all assemblies or not

[Dries-B]

When running this workflow, all samples are aligned to all assemblies. This is not always necessary and may cause unnecessary computational costs. Sometimes only mapping a sample to its own assembly may suffice.

Could a choice be incorporated in the config file and implemented in the workflow?

[Dries-B]

Note that this issue occurred when running workflow v2.3 (e007b32). I did not see commits that should have changed this behaviour since then.

[johnne]

Thanks for the suggestion! This has been implemented in 28 and, pending more testing, will soon be merged into the main branch.