Hey Simon!
Im starting using this command:
docker run --rm --user $(id -u):$(id -g) -v $(pwd):/zap/wrk/:rw -t softwaresecurityproject/zap-stable bash -c "zap.sh -cmd -addonupdate; zap.sh -cmd -autorun /zap/wrk/exported.yaml"
Hmm, I don't think the problem is that I can't access the file, it's not generating the file, I'm having a failure in the report generation job.