• Updated the nf-core release command
  • Now called nf-core bump-versions instead
  • New flag --nextflow to change the required nextflow version instead
• Template updates
  • Simpler installation of the nf-core helper tool, now directly from PyPI
  • Bump minimum nextflow version to 0.32.0 - required for built in manifest.nextflowVersion check and access to workflow.manifest variables from within nextflow scripts
  • New withName syntax for configs
  • Travis tests fail if PRs come against the master branch, slightly refactored
  • Improved GitHub contributing instructions and pull request / issue templates
• New lint tests
  • .travis.yml test for PRs made against the master branch
  • Automatic --release option not used if the travis repo is nf-core/tools
  • Warnings if depreciated variables params.version and params.nf_required_version are found
• New nf-core licences subcommand to show licence for each conda package in a workflow
• nf-core list now has options for sorting pipeline nicely
• Latest version of conda used in nf-core base docker image
• Updated PyPI deployment to correctly parse the markdown readme (hopefully!)
• New GitHub contributing instructions and pull request template

Very large release containing lots of work from the first nf-core hackathon, held in SciLifeLab Stockholm.

• The Cookiecutter template has been merged into tools
  • The old repo above has been archived
  • New pipelines are now created using the command nf-core create
  • The nf-core template and associated linting are now controlled under the same version system
• Large number of template updates and associated linting changes
  • New simplified cookicutter variable usage
  • Refactored documentation - simplified and reduced duplication
  • Better manifest variables instead of params for pipeline name and version
  • New integrated nextflow version checking
  • Updated travis docker pull command to use tagging to allow release tests to pass
  • Reverted Docker and Singularity syntax to use ENV hack again
• Improved Python readme parsing for PyPI
• Updated Travis tests to check that the correct dev branch is being targeted
• New sync tool to automate pipeline updates
  • Once initial merges are complete, a nf-core bot account will create PRs for future template updates

The version 1.0 of nf-core tools cannot be installed from PyPi. This patch fixes it, by getting rid of the requirements.txt plus declaring the dependent modules in the setup.py directly.

Initial release of the nf-core helper tools package. Currently includes four subcommands:

• nf-core list: List nf-core pipelines with local info
• nf-core download: Download a pipeline and singularity container
• nf-core lint: Check pipeline against nf-core guidelines
• nf-core release: Update nf-core pipeline version number