Fixes to run in July 2022

into -> set

PR checklist

[ ] This comment contains a description of changes (with reason)
[ ] CHANGELOG.md is updated
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] Documentation in docs is updated
[ ] If necessary, also make a PR on the nf-core/kmermaid branch on the nf-core/test-datasets repo