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 Tools helper code 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 Other Bump conda to 4.6.7 in base nf-core Dockerfil