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v2.0 - Palladium Platypus
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@KevinMenden KevinMenden released this 13 Jul 08:02
2.0
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v2.0 - Palladium Platypus - [2021-07-13]

⚠️ 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 <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.

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)
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