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v2.5 - Gold Otter
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@ewels ewels released this 30 Aug 13:29
· 3823 commits to master since this release
2.5
cd0ac0b

Full changelog: 2.4.1...2.5

Template

  • Bumped Python version to 3.7 in the GitHub linting in the workflow template (#1680)
  • Fix bug in pipeline readme logo URL (#1590)
  • Switch CI to use setup-nextflow action to install Nextflow (#1650)
  • Add CITATION.cff #361
  • Add Gitpod and Mamba profiles to the pipeline template (#1673)
  • Remove call to getGenomeAttribute in main.nf when running nf-core create without iGenomes (#1670)
  • Make nf-core create fail if Git default branch name is dev or TEMPLATE (#1705)
  • Convert console snippets to bash snippets in the template where applicable (#1729)
  • Add branch field to module entries in modules.json to record what branch a module was installed from (#1728)
  • Add customisation option to remove all GitHub support with nf-core create (#1766)

Linting

  • Check that the .prettierignore file exists and that starts with the same content.
  • Update readme.py nf version badge validation regexp to accept any signs before version number (#1613)
  • Add isort configuration and GitHub workflow (#1538)
  • Use black also to format python files in workflows (#1563)
  • Add check for mimetype in the input parameter. (#1647)
  • Check that the singularity and docker tags are parsable. Add --fail-warned flag to nf-core modules lint (#1654)
  • Handle exception in nf-core modules lint when process name doesn't start with process (#1733)

General

  • Remove support for Python 3.6 (#1680)
  • Add support for Python 3.9 and 3.10 (#1680)
  • Invoking Python with optimizations no longer affects the program control flow (#1685)
  • Update readme to drop --key option from nf-core modules list and add the new pattern syntax
  • Add --fail-warned flag to nf-core lint to make warnings fail (#1593)
  • Add --fail-warned flag to pipeline linting workflow (#1593)
  • Updated the nf-core package requirements (#1620, #1757, #1756)
  • Remove dependency of the mock package and use unittest.mock instead (#1696)
  • Fix and improve broken test for Singularity container download (#1622)
  • Use $XDG_CACHE_HOME or ~/.cache instead of $XDG_CONFIG_HOME or ~/config/ as base directory for API cache
  • Switch CI to use setup-nextflow action to install Nextflow (#1650)
  • Add tests for nf-core modules update and ModulesJson.
  • Add CI for GitLab remote #1646
  • Add CITATION.cff #361
  • Allow customization of the nf-core pipeline template when using nf-core create (#1548)
  • Add Refgenie integration: updating of nextflow config files with a refgenie database (#1090)
  • Fix --key option in nf-core lint when supplying a module lint test name (#1681)
  • Add no_git=True when creating a new pipeline and initialising a git repository is not needed in nf-core lint and nf-core bump-version (#1709)
  • Move strip_ansi_code function in lint to utils.py
  • Simplify control flow and don't use equality comparison for None and booleans
  • Replace use of the deprecated distutils Version object with that from packaging (#1735)
  • Add code to cancel CI run if a new run starts (#1760)
  • CI for the API docs generation now uses the ubuntu-latest base image (#1762)
  • Add option to hide progress bars in nf-core lint and nf-core modules lint with --hide-progress.

Modules

  • Add --fix-version flag to nf-core modules lint command to update modules to the latest version (#1588)
  • Fix a bug in the regex extracting the version from biocontainers URLs (#1598)
  • Update how we interface with git remotes. (#1626)
  • Add prompt for module name to nf-core modules info (#1644)
  • Update docs with example of custom git remote (#1645)
  • Command nf-core modules test obtains module name suggestions from installed modules (#1624)
  • Add --base-path flag to nf-core modules to specify the base path for the modules in a remote. Also refactored modules.json code. (#1643) Removed after (#1754)
  • Rename methods in ModulesJson to remove explicit reference to modules.json
  • Fix inconsistencies in the --save-diff flag nf-core modules update. Refactor nf-core modules update (#1536)
  • Fix bug in ModulesJson.check_up_to_date causing it to ask for the remote of local modules
  • Handle errors when updating module version with nf-core modules update --fix-version (#1671)
  • Make nf-core modules update --save-diff work when files were created or removed (#1694)
  • Get the latest common build for Docker and Singularity containers of a module (#1702)
  • Add short option for --no-pull option in nf-core modules
  • Add nf-core modules patch command (#1312)
  • Add support for patch in nf-core modules update command (#1312)
  • Add support for patch in nf-core modules lint command (#1312)
  • Add support for custom remotes in nf-core modules lint (#1715)
  • Make nf-core modules commands work with arbitrary git remotes (#1721)
  • Add links in README.md for info and patch commands (#1722])
  • Fix misc. issues with --branch and --base-path (#1726)
  • Add branch field to module entries in modules.json to record what branch a module was installed from (#1728)
  • Fix broken link in nf-core modules info(#1745)
  • Fix unbound variable issues and minor refactoring #1742
  • Recreate modules.json file instead of complaining about incorrectly formatted file. (#1741
  • Add support for patch when creating modules.json file (#1752)
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