nf-core/tools: v2.4 - Cobolt Koala

This release started off as a patch release to fix some errors introduced in 2.3 (eg. pipeline email template errors). However, it slowly collected enough new features to warrant a proper minor release of its own.

Many thanks to everyone who contributed!

Full Changelog: https://github.com/nf-core/tools/compare/2.3.2...2.4

• ✨ Add actions workflow to respond to @nf-core-bot fix linting comments on pipeline PRs
• Fix Prettier formatting bug in completion email HTML template (#1509)
• Fix bug in pipeline readme logo URL
• Set the default DAG graphic output to HTML to have a default that does not depend on Graphviz being installed on the host system (#1512).
• Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself
• Add .prettierignore file to stop Prettier linting tests from running over test files
• Made module template test command match the default used in nf-core modules create-test-yml (#1562)
• Removed black background from Readme badges now that GitHub has a dark mode, added Tower launch badge.
• Don't save md5sum for versions.yml when running nf-core modules create-test-yml (#1511)
• Read entire lines when sniffing the samplesheet format (fix #1561)

• ✨ Add actions workflow to respond to @nf-core-bot fix linting comments on nf-core/tools PRs
• Use $XDG_CONFIG_HOME or ~/.config/nf-core instead of ~/.nfcore for API cache (the latter can be safely deleted)
• Consolidate GitHub API calls into a shared function that uses authentication from the gh GitHub cli tool or GITHUB_AUTH_TOKEN to avoid rate limiting (#1499)
• Add an empty line to modules.json, params.json and nextflow-schema.json when dumping them to avoid prettier errors.
• Remove empty JSON schema definition groups to avoid usage errors (#1419)
• Bumped the minimum version of rich from v10 to v10.7.0

• ✨ Add a new command nf-core modules mulled which can generate the name for a multi-tool container image.
• ✨ Add a new command nf-core modules test which runs pytests locally.
• ✨ Print include statement to terminal when modules install (#1520)
• Allow follow links when generating test.yml file with nf-core modules create-test-yml (1570)
• Escaped test run output before logging it, to avoid a rich MarkupError

• Don't allow a .nf-core.yaml file, should be .yml (#1515).
• shell blocks now recognised to avoid error when: condition has too many lines (#1557)
• Fixed error when using comments after input tuple lines (#1542)
• Don't lint the shell block when script is used (1558)
• Check that template is used in script blocks
• Tweaks to CLI output display of lint results