I'm performing WGBS data analysis in plants using the Snakepipes WGBS pipeline. It uses bwa-meth for the mapping, MethylDackel to get the methylation levels and mbias correction and metilene to get the DMRs.
If you have a hard time installing the SnakePipes suite, you can create your own pipeline using these tools. Map the reads with bwa-meth, mark duplicates with sambamba, correct the Mbias with MethylDackel, get the CpG, CHG and CHH methylation levels with Methyldackel using the adequate parameters (--CHH --CHG), perform metilene analysis.
For SnakePipes to run you will need a Slurm queue, follow the SnakePipes installation parameters, modify SlurmEasy a bit for your cluster, createIndices for your reference genome (pipeline provided by SnakePipes). It's worthwhile in long run.