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  • The old repo above has been archived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