Bump nf-core from 2.1 to 2.5.1

[dependabot]

Bumps nf-core from 2.1 to 2.5.1.

Release notes

Sourced from nf-core's releases.

v2.5.1 - Gold Otter Patch

This release fixes a sync error with Black linting in pipelines.

• Patch release to fix black linting in pipelines (nf-core/tools#1789)
• Add isort options to pyproject.toml (nf-core/tools#1792)
• Lint pyproject.toml file exists and content (nf-core/tools#1795)
• Update GitHub PyPI package release action to v1 (nf-core/tools#1785)

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

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.5.1 - Gold Otter Patch - [2022-08-31]

• Patch release to fix black linting in pipelines (#1789)
• Add isort options to pyproject.toml (#1792)
• Lint pyproject.toml file exists and content (#1795)
• Update GitHub PyPI package release action to v1 (#1785)

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)

... (truncated)

Commits

• bc56cdd Generate new screengrabs with rich-codex
• cf280d6 Merge pull request #1793 from nf-core/dev
• ee6b104 Merge pull request #1788 from fabianegli/black-default-compliant
• 9d30b2b remove unnecessary f-string
• 8d9bae6 be compliant with black defaults
• b48be11 Merge pull request #1794 from mirpedrol/patch2.5.1
• f31c9e9 Merge branch 'dev' into patch2.5.1
• 2d7360f Update CHANGELOG.md
• ec60f53 Merge pull request #1795 from mirpedrol/lint-pyproject
• d5cbde0 update changelog
• Additional commits viewable in compare view

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[dependabot]

Superseded by #60.