Release 5.1.0

[rhpvorderman]

• Check outstanding issues on JIRA and Github.
• 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".
• Check all submodules are tagged correctly with git submodule.
• Run tests to confirm to be released version works.
• Generate inputs overview using wdl-aid:
  wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
• 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.
• Check latest documentation looks fine.
• Change current development version in CHANGELOG.md to stable version.
• 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.
• 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.
• Create a new release from the pushed tag on github.
• Prepare the repo for packaging
  by git checkout master && git submodule update --init --recursive.
  • Package the wdl files with wdl-packager --reproducible -a LICENSE -a dockerImages.yml <WDL_FILE>.
  • Add the package(s) to the github release. Also add the original WDL
    file as <pipeline>_<version>.wdl following the same naming as the
    package.
    This alllows for usage of wdl and imports zip with cromwell without
    requiring the user to extract the package.