nf-core/tools: 1.5 - Iron Shark

Template pipeline

• Dropped Singularity file
• Summary now logs details of the cluster profile used if from nf-core/configs
• Dockerhub is used in favor of Singularity Hub for pulling when using the Singularity profile
• Changed default container tag from latest to dev
• Brought the logo to life
• Change the default filenames for the pipeline trace files
• Remote fetch of nf-core/configs profiles fails gracefully if offline
• Remove params.container and just directly define process.container now
• Completion email now includes MultiQC report if not too big
• params.genome is now checked if set, to ensure that it's a valid iGenomes key
• Together with nf-core/configs, helper function now checks hostname and suggests a valid config profile

• New nf-core launch command to interactively launch nf-core pipelines from command-line
  • Works with a parameters.settings.json file shipped with each pipeline
  • Discovers additional params from the pipeline dynamically
• Drop Python 3.4 support
• nf-core list now only shows a value for "is local latest version" column if there is a local copy.
• Lint markdown formatting in automated tests
  • Added markdownlint-cli for checking Markdown syntax in pipelines and tools repo
• Syncing now reads from a blacklist.json in order to exclude pipelines from being synced if necessary.
• Added nf-core tools API description to assist developers with the classes and functions available.
  • Docs are automatically built by Travis CI and updated on the nf-co.re website.
• Introduced test for filtering remote workflows by keyword.

• Build tools python API docs

  • Use Travis job for api doc generation and publish

• nf-core bump-version now stops before making changes if the linting fails

• Code test coverage
  • Introduced test for filtering remote workflows by keyword
• Linting updates
  • Now properly searches for conda packages in default channels
  • Now correctly validates version pinning for packages from PyPI
  • Updates for changes to process.container definition

• Bump conda to 4.6.7 in base nf-core Dockerfile