1.9 - Platinum Pigeon

Continuous integration

• Travis CI tests are now deprecated in favor of GitHub Actions within the pipeline template.
  • nf-core bump-version support has been removed for .travis.yml
  • nf-core lint now fails if a .travis.yml file is found
• Ported nf-core/tools Travis CI automation to GitHub Actions
• Fixed the build for the nf-core/tools API documentation on the website

Template

• Rewrote the documentation markdown > HTML conversion in Python instead of R
• Removed the requirement for R in the conda environment
• Make params.multiqc_config give an additional MultiQC config file instead of replacing the one that ships with the pipeline
• Ignore only tests/ and testing/ directories in .gitignore to avoid ignoring test.config configuration file
• Rephrase docs to promote usage of containers over Conda to ensure reproducibility
• Stage the workflow summary YAML file within MultiQC work directory

Linting

• Removed linting for CircleCI
• Allow any one of params.reads or params.input or params.design before warning
• Added whitespace padding to lint error URLs
• Improved documentation for lint errors
• Allow either >= or !>= in nextflow version checks (the latter exits with an error instead of just warning) #506
• Check that manifest.version ends in dev and throw a warning if not
  • If running with --release check the opposite and fail if not
• Tidied up error messages and syntax for linting GitHub actions branch tests
• Add YAML validator
• Don't print test results if we have a critical error

Other

• Fix automatic synchronisation of the template after releases of nf-core/tools
• Improve documentation for installing nf-core/tools
• Replace preprint by the new nf-core publication in Nature Biotechnology 🍾
• Use stderr instead of stdout for header artwork
• Tolerate unexpected output from nextflow config command
• Add social preview image
• Added a release checklist for the tools repo