Spider runs at the start and finish at the end of all the pipelines.
Spider caches web pages which are used throughout the pipeline and sets an environment variable, so that all launched jobs can access them.
Finish is very important, as it ties off the log files, and writes a json string of the processes launched, which is needed for the schema generation.
Status changes have been left out, along with some file checking and creation of tag specific lane files which occur at the start of the primary analysis pipelines. These happen, but are not responsible directly for the files and qc that you see.
The production version of the primary pipeline launches a version of the secondary pipeline which creates a Latest_Summary link to it's archival files and QC.