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 Template Move TODO item of contains: map in a YAML string [#1082] Trigger AWS tests via Tower API [#1160] General 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 Modules 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 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. Sync Don't set the default value to "null" when a parameter is initialised as null in the config [#1074] Tests 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