Bump nf-core from 2.1 to 2.7.1

[dependabot]

Bumps nf-core from 2.1 to 2.7.1.

Release notes

Sourced from nf-core's releases.

v2.7.1 - Mercury Eagle Patch

This release fixes a sync error with the new syntax of set_output on GitHub Actions.

• Patch release to fix pipeline sync (#2110)

v2.7 - Mercury Eagle

Another big release with lots of new features and bug fixes. Thanks to all contributors!

🌟 Highlights

• New nf-core subworkflows subcommand for creating, removing, testing, updating and finding subworkflows, see the documentation for more information.
• Every pipeline has now it's own GitHub codespace template, which can be used to develop the pipeline directly in the browser.
• Improved handling of modules and subworkflows from other repos than nf-core/modules.
• Pre-commit is now installed as a dependency, which allows us, besides other things, to run prettier on the fly even if it is not manually installed.
• Shell completion for nf-core commands, more information here.

Template

Features

• Ignore files in bin/ directory when running prettier (#2080).
• Add GitHub codespaces template (#1957)
• nextflow run <pipeline> --version will now print the workflow version from the manifest and exit (#1951).
• Add profile for running docker with the ARM chips (including Apple silicon) (#1942 and #2034).
• Flip execution order of parameter summary printing and parameter validation to prevent 'hiding' of parameter errors (#2033).
• Change colour of 'pipeline completed successfully, but some processes failed' from red to yellow (#2096).

Bug fixes

• Fix lint warnings for samplesheet_check.nf module (#1875).
• Check that the workflow name provided with a template doesn't contain dashes (#1822)
• Remove CITATION.cff file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline (#2059).

Linting

Features

• Add --sort-by option to linting which allows ordering module lint warnings/errors by either test name or module name (#2077).

Bug fixes

• Don't lint pipeline name if manifest.name in .nf-core.yml (#2035)
• Don't check for docker pull commands in actions_ci lint test (leftover from DSL1) (#2055).

General

Features

• Use pre-commit run prettier if prettier is not available (#1983) and initialize pre-commit in gitpod and codespaces (#1957).
• Refactor CLI flag --hide-progress to be at the top-level group, like --verbose (#2016)

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.7.1 - Mercury Eagle Patch - [2022-12-08]

• Patch release to fix pipeline sync (#2110)

v2.7 - Mercury Eagle - [2022-12-07]

Another big release with lots of new features and bug fixes. Thanks to all contributors!

Highlights

• New nf-core subworkflows subcommand for creating, removing, testing, updating and finding subworkflows, see the documentation for more information.
• Every pipeline has now it's own GitHub codespace template, which can be used to develop the pipeline directly in the browser.
• Improved handling of modules and subworkflows from other repos than nf-core/modules.
• Pre-commit is now installed as a dependency, which allows us, besides other things, to run prettier on the fly even if it is not manually installed.
• Shell completion for nf-core commands, more information here.

Template

Features

• Ignore files in bin/ directory when running prettier (#2080).
• Add GitHub codespaces template (#1957)
• nextflow run <pipeline> --version will now print the workflow version from the manifest and exit (#1951).
• Add profile for running docker with the ARM chips (including Apple silicon) (#1942 and #2034).
• Flip execution order of parameter summary printing and parameter validation to prevent 'hiding' of parameter errors (#2033).
• Change colour of 'pipeline completed successfully, but some processes failed' from red to yellow (#2096).

Bug fixes

• Fix lint warnings for samplesheet_check.nf module (#1875).
• Check that the workflow name provided with a template doesn't contain dashes (#1822)
• Remove CITATION.cff file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline (#2059).

Linting

Features

• Add --sort-by option to linting which allows ordering module lint warnings/errors by either test name or module name (#2077).

Bug fixes

• Don't lint pipeline name if manifest.name in .nf-core.yml (#2035)
• Don't check for docker pull commands in actions_ci lint test (leftover from DSL1) (#2055).

General

Features

• Use pre-commit run prettier if prettier is not available (#1983) and initialize pre-commit in gitpod and codespaces (#1957).
• Refactor CLI flag --hide-progress to be at the top-level group, like --verbose (#2016)

... (truncated)

Commits

• eecf1c7 Generate new screengrabs with rich-codex
• 71d7913 Merge pull request #2112 from nf-core/dev
• 54aee22 Merge pull request #2111 from mirpedrol/2.7.1
• 1f462a8 Merge branch 'dev' into 2.7.1
• b43f97a Merge pull request #2110 from mirpedrol/sync-yml
• 8c0c718 fix typo
• ebd0b2d bump to version 2.7.1
• f3195ed fix new syntax form set_output in sync.yml
• 5c4477b Generate new screengrabs with rich-codex
• 58da1e3 Merge pull request #2107 from nf-core/dev
• Additional commits viewable in compare view

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[dependabot]

Superseded by #65.