It would be nice to add a params to choose the VEP genome assembly.
In most cases it is the --genome params, but I'm assuming it'll be easier to control if we have that as a separate params.
For example, it's currently not working with the --genome custom setting.

I think it would be good to have a module for gatk4

Hi there,
I wonder if it would be possible to add a feature in the pipeline allowing libraries made with different adapter sequences to be processed in the same run.

For example, my colleagues and I are often working with a mixture of Illumina and BGI (4 channel) sequencing data and it would be cool to be able run these data together, instead of having to run adapter removal separately for eac