About biobakery workflow

Hello all,
I’m new to shotgun metagenomics data analysis, so sorry for my questions!
I’ve paired end fastq.gz files R1 and R2

I’ve few questions about the process of biobakery workflow,
should I merge the reads(R1&R2) in a single file per sample before running the workflow command? If so, could you please recommend a tool for that?

for the preprocessing the raw data, if the following command is used;
biobakery_workflows wmgx --input OUTPUT_DATA,
How the tool KneadData predicts the adapter to be removed? should I do a step before to prepare files for this step (e.g. remove the adapter with Trimmomatic tool then use its outputs files as input for the the biobakery workflow) or modify the command?

Thanking you help

Could someone please help?