Bump nf-core from 2.1 to 2.8

[dependabot]

Bumps nf-core from 2.1 to 2.8.

Release notes

Sourced from nf-core's releases.

v2.8 - Ruthenium Monkey

v2.8 - Ruthenium Monkey - [2023-04-27]

Template

• Explicitly disable conda when a container profile (#2140)
• Turn on automatic clean up of intermediate files in work/ on successful pipeline completion in full-test config (#2163) [Contributed by @​jfy133]
• Add documentation to usage.md on how to use params.yml files, based on nf-core/ampliseq text (#2173) [Contributed by @​jfy133, @​d4straub]
• Make jobs automatically resubmit for a much wider range of exit codes (now 104 and 130..145) (#2170)
• Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
• Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://redirect.github.com/Remove dodgy sniffer code from samplesheet_check.py nf-core/tools#2194]) [Contributed by @​Midnighter, @​jfy133]
• Consistent syntax for branch checks in PRs (#2202)
• Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
• Updated AWS tests to use newly moved seqeralabs/action-tower-launch instead of nf-core/tower-action
• Remove .cff files from .editorconfig [(#2145)[https://redirect.github.com/Update .editorconfig nf-core/tools#2145]]
• Simplify pipeline README (#2186)
• Added support for the apptainer container engine via -profile apptainer. (#2244) [Contributed by @​jfy133]
• Added config docker.registry to pipeline template for a configurable default container registry when using Docker containers. Defaults to quay.io (#2133)
• Add tower.yml file to the pipeline template (#2251)
• Add mastodon badge to README (#2253)
• Removed quay.io from all module Docker container references as this is now supplied at pipeline level. (#2249)
• Remove CITATION.cff file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline (#2059).

Linting

• Update modules lint test to fail if enable_conda is found (#2213)
• Read module lint configuration from .nf-core.yml, not .nf-core-lint.yml (#2221)
• nf-core schema lint now defaults to linting nextflow_schema.json if no filename is provided (#2225)
• Warn if /zenodo.XXXXXX is present in the Readme (#2254)
• Lint all labels in a module (#2227)

Modules

• Add an --empty-template option to create a module without TODO statements or examples (#2175 & #2177)
• Removed the nf-core modules mulled command and all its code dependencies (2199).
• Take into accout the provided --git_remote URL when linting all modules (2243).

Subworkflows

• Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL (#2177)
• Fix nf-core subworkflows test not running subworkflow tests (#2181)
• Add tests for nf-core subworkflows create-test-yml (#2219)

General

• Deprecate Python 3.7 support because it reaches EOL (#2210)
• nf-core modules/subworkflows info now prints the include statement for the module/subworkflow (#2182).
• Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
• update minimum version of rich to 13.3.1 (#2185)
• Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to nextflow.config) (#2196)

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.8 - Ruthenium Monkey - [2023-04-27]

Template

• Explicitly disable conda when a container profile (#2140)
• Turn on automatic clean up of intermediate files in work/ on successful pipeline completion in full-test config (#2163) [Contributed by @​jfy133]
• Add documentation to usage.md on how to use params.yml files, based on nf-core/ampliseq text (#2173) [Contributed by @​jfy133, @​d4straub]
• Make jobs automatically resubmit for a much wider range of exit codes (now 104 and 130..145) (#2170)
• Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
• Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://redirect.github.com/Remove dodgy sniffer code from samplesheet_check.py nf-core/tools#2194]) [Contributed by @​Midnighter, @​jfy133]
• Consistent syntax for branch checks in PRs (#2202)
• Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
• Updated AWS tests to use newly moved seqeralabs/action-tower-launch instead of nf-core/tower-action
• Remove .cff files from .editorconfig [(#2145)[https://redirect.github.com/Update .editorconfig nf-core/tools#2145]]
• Simplify pipeline README (#2186)
• Added support for the apptainer container engine via -profile apptainer. (#2244) [Contributed by @​jfy133]
• Added config docker.registry to pipeline template for a configurable default container registry when using Docker containers. Defaults to quay.io (#2133)
• Add tower.yml file to the pipeline template (#2251)
• Add mastodon badge to README (#2253)
• Removed quay.io from all module Docker container references as this is now supplied at pipeline level. (#2249)
• Remove CITATION.cff file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline (#2059).

Linting

• Update modules lint test to fail if enable_conda is found (#2213)
• Read module lint configuration from .nf-core.yml, not .nf-core-lint.yml (#2221)
• nf-core schema lint now defaults to linting nextflow_schema.json if no filename is provided (#2225)
• Warn if /zenodo.XXXXXX is present in the Readme (#2254)
• Lint all labels in a module (#2227)

Modules

• Add an --empty-template option to create a module without TODO statements or examples (#2175 & #2177)
• Removed the nf-core modules mulled command and all its code dependencies (2199).
• Take into accout the provided --git_remote URL when linting all modules (2243).

Subworkflows

• Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL (#2177)
• Fix nf-core subworkflows test not running subworkflow tests (#2181)
• Add tests for nf-core subworkflows create-test-yml (#2219)

General

• Deprecate Python 3.7 support because it reaches EOL (#2210)
• nf-core modules/subworkflows info now prints the include statement for the module/subworkflow (#2182).
• Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
• update minimum version of rich to 13.3.1 (#2185)
• Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to nextflow.config) (#2196)
• Use nfcore/gitpod:dev container in the dev branch (#2196)

... (truncated)

Commits

• 0912990 Merge pull request #2257 from nf-core/dev
• 7a7a326 Merge pull request #2266 from mirpedrol/newline-fix
• 7c6c51d fix template new lines
• e48bb35 Generate new screengrabs with rich-codex
• 20d0782 Merge pull request #2265 from mashehu/fix-rich-code
• b4f103c update subworkflow commands for rich-codex
• df27c28 Generate new screengrabs with rich-codex
• 81e8278 Merge pull request #2264 from mirpedrol/update-dumpsoftwareversions
• c40ad45 update dumpsoftwareversions permisions
• fe2c5e8 Merge pull request #2263 from mashehu/fix-template-modules
• Additional commits viewable in compare view

You can trigger a rebase of this PR by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

> **Note** > Automatic rebases have been disabled on this pull request as it has been open for over 30 days.

[dependabot]

Superseded by #71.