Bump nf-core from 2.1 to 2.7.2

[dependabot]

Bumps nf-core from 2.1 to 2.7.2.

Release notes

Sourced from nf-core's releases.

v2.7.2 - Mercury Eagle Patch

v2.7.2 - Mercury Eagle Patch

Patch release solving some bugs introduced with v2.7

Template

• Fix the syntax of github_output in GitHub actions (#2114)
• Fix a bug introduced in 2.7 that made pipelines hang (#2132)

Linting

• Allow specifying containers in less than three lines (#2121)
• Run prettier after dumping a JSON schema file (#2124)

General

• Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of --name. Don't check if a template file is used. (#2123)
• Deprecate --enable_conda parameter. Use conda.enable instead (#2131)
• Handle json.load() exceptions (#2134)

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

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.7.2 - Mercury Eagle Patch - [2022-12-19]

Template

• Fix the syntax of github_output in GitHub actions (#2114)
• Fix a bug introduced in 2.7 that made pipelines hang (#2132)

Linting

• Allow specifying containers in less than three lines (#2121)
• Run prettier after dumping a json schema file (#2124)

General

• Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of --name. Don't check if a template file is used. (#2123)
• Deprecate --enable_conda parameter. Use conda.enable instead (#2131)
• Handle json.load() exceptions (#2134)

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).

... (truncated)

Commits

• 99961be Generate new screengrabs with rich-codex
• 9d7dbee Merge pull request #2136 from nf-core/dev
• 9e6b67f Merge pull request #2135 from mirpedrol/bump-2.7.2
• 02acf65 bump to 2.7.2 for patch release
• d45b8e3 Merge pull request #2134 from mirpedrol/handle-json-exception
• b33d0c7 Merge pull request #2131 from mirpedrol/conda-enable
• 81fc966 remove params.enable_conda from modules template
• 0cb35e6 check conda channels as it's done in rnaseq
• 32bf4aa Merge branch 'dev' of https://github.com/nf-core/tools into conda-enable
• 632b675 remove handling from linting as it's already handled later
• Additional commits viewable in compare view

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[dependabot]

Superseded by #69.