1.4 - Tantalum Butterfly

Template pipeline

• Institutional custom config profiles moved to github nf-core/configs
  • These will now be maintained centrally as opposed to being shipped with the pipelines in conf/
  • Load base.config by default for all profiles
  • Removed profiles named standard and none
  • Added parameter --igenomesIgnore so igenomes.config is not loaded if parameter clashes are observed
  • Added parameter --custom_config_version for custom config version control. Can use this parameter to provide commit id for reproducibility. Defaults to master
  • Deleted custom configs from template in conf/ directory i.e. uzh.config, binac.config and cfc.config
• multiqc_config and output_md are now put into channels instead of using the files directly (see issue #222)
• Added local.md to cookiecutter template in docs/configuration/. This was referenced in README.md but not present.
• Major overhaul of docs to add/remove parameters, unify linking of files and added description for providing custom configs where necessary
• Travis: Pull the dev tagged docker image for testing
• Removed UPPMAX-specific documentation from the template.

Tools helper code

• Make Travis CI tests fail on pull requests if the CHANGELOG.md file hasn't been updated
• Minor bugfixing in Python code (eg. removing unused import statements)
• Made the web requests caching work on multi-user installations
• Handle exception if nextflow isn't installed
• Linting: Update for Travis: Pull the dev tagged docker image for testing