nf-core/tools: v2.0 - Palladium Platypus

v2.0 - Palladium Platypus - [2021-07-13] :warning: Major enhancements & breaking changes

This marks the first Nextflow DSL2-centric release of tools which means that some commands won't work in full with DSL1 pipelines anymore. Please use a v1.x version of tools for such pipelines or better yet join us to improve our DSL2 efforts! Here are the most important changes:

• The pipeline template has been completely re-written in DSL2
• A module template has been added to auto-create best-practice DSL2 modules to speed up development
• A whole suite of commands have been added to streamline the creation, installation, removal, linting and version bumping of DSL2 modules either installed within pipelines or the nf-core/modules repo

• Move TODO item of contains: map in a YAML string [#1082]
• Trigger AWS tests via Tower API [#1160]

• Fixed a bug in the Docker image build for tools that failed due to an extra hyphen. [#1069]
• Regular release sync fix - this time it was to do with JSON serialisation [#1072]
• Fixed bug in schema validation that ignores upper/lower-case typos in parameters [#1087]
• Bugfix: Download should use path relative to workflow for configs
• Remove lint checks for files related to conda and docker as not needed anymore for DSL2
• Removed params_used lint check because of incompatibility with DSL2
• Addedmodules bump-versions command to README.md
• Update docs for v2.0 release

• Update comment style of modules functions.nf template file [#1076]
• Changed working directory to temporary directory for nf-core modules create-test-yml [#908]
• Use Biocontainers API instead of quayi.io API for nf-core modules create [#875]
• Update nf-core modules install to handle different versions of modules #1116
• Added nf-core modules bump-versions command to update all versions in the nf-core/modules repository [#1123]
• Updated nf-core modules lint to check whether a git_sha exists in the modules.json file or whether a new version is available [#1114]
• Refactored nf-core modules command into one file per command #1124
• Updated nf-core modules remove to also remove entry in modules.json file (#1115)
• Bugfix: Interactive prompt for nf-core modules install was receiving too few arguments
• Added progress bar to creation of 'modules.json'
• Updated nf-core modules list to show versions of local modules
• Improved exit behavior by replacing sys.exit with exceptions
• Updated nf-core modules remove to remove module entry in modules.json if module directory is missing
• Create extra tempdir as work directory for nf-core modules create-test-yml to avoid adding the temporary files to the test.yml
• Refactored passing of command line arguments to nf-core commands and subcommands (#1139, #1140)
• Check for modules.json for entries of modules that are not actually installed in the pipeline [#1141]
• Added <keywords> argument to nf-core modules list for filtering the listed modules. (#1139
• Added support for a bump-versions configuration file [#1142]
• Fixed nf-core modules create-test-yml so it doesn't break when the output directory is supplied [#1148]
• Updated nf-core modules lint to work with new directory structure [#1159]
• Updated nf-core modules install and modules.json to work with new directory structure (#1159)
• Updated nf-core modules remove to work with new directory structure [#1159]
• Restructured code and removed old table style in nf-core modules list
• Fixed bug causing modules.json creation to loop indefinitly
• Added --all flag to nf-core modules install
• Added remote and local subcommands to nf-core modules list
• Fix bug due to restructuring in modules template
• Added checks for verifying that the remote repository is well formed
• Added checks to ModulesCommand for verifying validity of remote repositories
• Misc. changes to modules install: check that module exist in remote, --all is has --latest by default.

• Don't set the default value to "null" when a parameter is initialised as null in the config [#1074]

• Added a test for the version_consistency lint check
• Refactored modules tests into separate files, and removed direct comparisons with number of tests in lint tests (#1158)