poly-A trimming for paired-end data - consider orientation

[benemead]

Thanks @marcelm for maintaining such a useful tool!

Regarding the relatively new poly-A trimming feature - would it be possible to toggle strandedness?

By default you consider R1 to have the polyA and R2 to have polyT but for applications such as single cell RNA-seq, it can often be the opposite.

[marcelm]

Thanks for the feedback!

As a workaround, you can swap the R1 and R2 input and output files and the read-specific options (such as -a ↔ -A and -m ↔ -M).

This workoraund gets confusing quickly, so I will definitely think about how to make this configurable.

[benemead]

yep, that's what I've been doing 👍