It looks like these three tests fail because of two issues
1) There is no web service running when seqware-pipeline is tested
2) BamQC doesn't exist in our test database, if you want it, you'll need to create it first

This test class should be moved to seqware-webservice. There are a few utilities in the tests there that will set your metadata to use the embedded web service correctly (here it looks like you will just trust whatever is in your .seqware/settings file). Feel free to swing by my desk in order to work on this together if you get stuck.