Three different reports were generated by the workflows: a trimming report and two QC reports. All of these should be inspected in order to determine whether the quality of the sequencing reads and the trimming are acceptable. The interpretation of the reports is not always completely straightforward, but as you gain experience it becomes easier. For a detailed description of the QC reports and indication on how to interpret the different values, see QC Sequencing Report Content. For the trimming report, Trim output.
If you can accept the read quality you can now proceed to the next step and use the prepared reads output as input in the next ready-to-use workflow. If the quality of your reads is poor and cannot be accepted for further analysis, the best solution to the problem is to go back to start and resequence the sample.
You are now ready to perform the actual analysis of your sequencing data.