Bump nf-core from 2.1 to 2.5

[dependabot]

Bumps nf-core from 2.1 to 2.5.

Release notes

Sourced from nf-core's releases.

v2.5 - Gold Otter

Full changelog: nf-core/tools@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)

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.5 - Gold Otter - [2022-08-30]

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)

... (truncated)

Commits

• cd0ac0b Generate new screengrabs with rich-codex
• 57e27cf Merge pull request #1782 from nf-core/dev
• 04a699a Merge pull request #1781 from ewels/master
• c5ddf28 Bump to v2.5 for release
• a5c5b58 Merge pull request #1773 from fabianegli/fix-anomalous-bakslash
• 9a28bfa Merge branch 'dev' into fix-anomalous-bakslash
• 174a612 Merge pull request #1772 from mirpedrol/no-git
• a2111ba Merge branch 'dev' into no-git
• b279396 Merge pull request #1779 from mashehu/remove-change-thresholds
• cdd7b58 forget it, we are doing it manually
• Additional commits viewable in compare view

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[dependabot]

Superseded by #58.