Bump nf-core from 2.1 to 2.4.1

[dependabot]

Bumps nf-core from 2.1 to 2.4.1.

Release notes

Sourced from nf-core's releases.

v2.4.1 - Cobolt Koala Patch

Somehow it wouldn't feel like a real nf-core/tools release if there wasn't some error with the automatic template sync that required an immediate patch release.. 🤔

Hopefully this release will fill everyone's inboxes with automated update pull requests.. 🤞🏻

• Patch release to try to fix the template sync (#1585)
• Avoid persistent temp files from pytests (#1566)
• Add option to trigger sync manually on just nf-core/testpipeline

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: nf-core/tools@2.3.2...2.4

Template

• ✨ 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)

General

• ✨ 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

Modules

• ✨ 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

Linting

• 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)

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.4.1 - Cobolt Koala Patch - [2022-05-16]

• Patch release to try to fix the template sync (#1585)
• Avoid persistent temp files from pytests (#1566)
• Add option to trigger sync manually on just nf-core/testpipeline

v2.4 - Cobolt Koala - [2022-05-16]

Template

• Read entire lines when sniffing the samplesheet format (fix #1561)
• 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)

General

• 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

Modules

• 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

Linting

• 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

v2.3.2 - Mercury Vulture Fixed Formatting - [2022-03-24]

Very minor patch release to fix the full size AWS tests and re-run the template sync, which partially failed due to GitHub pull-requests being down at the time of release.

... (truncated)

Commits

• 171127b Merge pull request #1587 from nf-core/dev
• 0638904 Shh 🤫
• 74eb853 Merge pull request #1586 from nf-core/dev
• 0fbe429 Add option to trigger sync manually on just nf-core/testpipeline
• 57b3cf7 Changelog entry
• a77e22d Merge pull request #1585 from ewels/fix-2.4-sync
• d39897b Fix logging error in get request
• f8a451b Bump version to 2.4.1
• 1f0c8c7 Minor tweaks
• 244e4a0 Sync: additional log messages
• Additional commits viewable in compare view

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[dependabot]

Superseded by #57.