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 :champagne: 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