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Published February 20, 2020 | Version 1.9
Software Open

nf-core/tools: 1.9 - Platinum Pigeon

Authors/Creators

  • 1. Science for Life Laboratory
  • 2. QBiC @qbicsoftware
  • 3. The Francis Crick Institute
  • 4. Boehringer Ingelheim
  • 5. @SciLifeLab | Karolinska Institutet
  • 6. @qbicsoftware
  • 7. @Gregor-Mendel-Institute
  • 8. Max Planck Institute for the Science of Human History
  • 9. @czbiohub
  • 10. Max Planck institute for the Science of Human Evolution
  • 11. @SGBC
  • 12. Zymo Research Corp.
  • 13. @ScilifelabDataCentre
  • 14. Harvard Chan School of Public Health
  • 15. @NBISweden
  • 16. @OICR_news

Description

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

Files

nf-core/tools-1.9.zip

Files (299.6 kB)

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md5:ab6e945b00d518c51ccac48aa89aeb74
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Additional details

Related works

Is supplement to
https://github.com/nf-core/tools/tree/1.9 (URL)