v4.2.0 - Metropolitan Mouse

Highlights:

• Metro maps with manifest.diagram in the nextflow.config file
• New command: nf-core pipelines containers create-configs

General

• Fixes bug in test-datasets list related to broken rich import (#4477)
• Add nf-core pipelines containers create-configs to regenerate the pipeline conf/containers_*.config files (#XXXX)
• update update-*-snapshot actions to more robust way (#4509)

Linting

• Warn if manifest.diagram is not set, and fail if it is not a relative path to an existing image file (#4460)
• Add strandeness to permitted meta keys (#4473)
• remove ext.use_gpu as a permitted ext key, superseded by task.accelerator (#4445)
• fix(lint): use repo-root-relative path in git restore call in container_configs (#4301)
• Fix subworkflow lint parsing sibling subworkflow include statements (#4527)

Modules

• modules main.nf template: match nf-core container formatting in main.nf (#4459)

Template

• remove redundant ext.use_gpu from the process_gpu label, use accelerator only (#4445)
• Switch to using fix-linting.yml workflow from nf-core/actions repo, to avoid leakage of nf-core bot token and rename it from fix_linting.yml to fix-linting.yml (#4485)
• Add a commented-out manifest.diagram to nextflow.config, for the pipeline metro map (#4460)
• git-ignore nf-test files (#4461)
• Bump nf-schema to 2.7.3 to allow running pipelines with Nextflow 26.04 (#4463)
• Bump nft-utils to 1.2.1, matching nf-core/modules (#4489)
• VSCode: add recommended extensions, fix link to admonition styling CSS for markdown previews (#4455)
• Pin action-tower-launch to v2 (#4502)
• Pin nf-schema version in awsfulltest (#4501)
• Don't block workflow.onComplete on the MultiQC report (#4486)