Release 3.1.0

[rhpvorderman]

Release checklist

• [x] Check outstanding issues on JIRA and Github
• [x] Update all submodules to latest master with: git submodule foreach "git checkout master;git pull; git submodule foreach --recursive 'git fetch'; git submodule update --init --recursive"
• [x] check all submodules are tagged correctly with git submodule
• [x] run tests to confirm to be released version works.
• [x] Generate inputs overview using wdl-aid: wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
• [x] Publish documentation (updateDocs.sh) from develop branch
  • [ ] Copy docs folder to gh-pages branch
  • [ ] Overwrite existing develop folder with docs folder on gh-pages
  • [ ] Push changes to gh-pages branch
• [x] Check latest documentation looks fine
• [x] Change current development version in CHANGELOG.md to stable version.
• [x] Run the release script release.sh
  • [ ] Check all submodules are tagged
  • [ ] Merge the develop branch into master
  • [ ] Created an annotated tag with the stable version number. Include changes from changelog.md.
  • [ ] Confirm or set stable version to be used for tagging
  • [ ] Push tag to remote.
  • [ ] Merge master branch back into develop.
  • [ ] Add updated version number to develop
• [x] Publish documentation (updateDocs.sh) from master branch
  • [ ] Copy docs folder to gh-pages branch
  • [ ] Rename docs to new stable version on gh-pages
  • [ ] Set latest version to new version
  • [ ] Push changes to gh-pages branch
• [x] Create a new release from the pushed tag on github