Why have fastqc and trimmomatic been deprecated and what should I use as a replacement?
None of the two has been deprecated afaik. Where did you get this information?
edit: I see what you mean now, the tool panel on usegalaxy.org seems mixed, we will fix it. The tools are not deprecated, just positioned wrongly in the panel.
Thank you, marten.
It has been fixed, thanks for reporting it.