I am no networking expert, so I can't explain the setup is fine detail, but every request must be passed to the proxy along with a username and password, otherwise the proxy immediately returns 407 and the request goes nowhere. To make the credentials available to programs, they are saved in env variables HTTP_PROXY and HTTPS_PROXY. Python respects these variables, so the tools work as intended. git also works normally. However, Nextflow and Wave rely on some Java machinery that seemingly ignores those variables, and hence all requests originating from Nextflow are rejected. I would love to provide an MWE but I have no idea on how to reproduce the network setup.