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v3.1.0 - Brass Boxfish

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@mirpedrol mirpedrol released this 12 Dec 11:01
3.1.0
8232947
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⭐ Highlights ⭐

  • We added the new contributors field to the pipeline template manifest.
  • The nf-core pipelines download command supports ORAS container URIs.
  • New command nf-core subworkflows patch.

Template

  • Keep pipeline name in version.yml file (#3223)
  • Fix Manifest DOI text (#3224)
  • Do not assume pipeline name is url (#3225)
  • fix workflow_dispatch trigger and parse more review comments in awsfulltest (#3235)
  • Add resource limits to Gitpod profile(#3255)
  • Fix a typo (#3268)
  • Remove def from nextflow.config and add trace_report_suffix param (#3296)
  • Move includeConfig 'conf/modules.config' next to includeConfig 'conf/base.config' to not overwrite tests profiles configurations (#3301)
  • Use params.monochrome_logs in the template and update nf-core components (#3310)
  • Fix some typos and improve writing in usage.md and CONTRIBUTING.md (#3302)
  • Add manifest.contributors to nextflow.config (#3311)
  • Update template components (#3328)
  • Template: Remove mention of GRCh37 if igenomes is skipped (#3330)
  • Be more verbose in approval check action (#3338)

Download

  • First steps towards fixing #3179: Modify prioritize_direct_download() to retain Seqera Singularity https:// Container URIs and hardcode Seqera Containers into gather_registries() (#3244).
  • Further steps towards fixing #3179: Enable limited support for oras:// container paths (only absolute URIs, no flexible registries like with Docker) and prevent unnecessary image downloads for Seqera Container modules with reconcile_seqera_container_uris() (#3293).
  • Update dawidd6/action-download-artifact action to v7 (#3306)

Linting

  • allow mixed str and dict entries in lint config (#3228)
  • fix meta_yml linting test failing due to module.process_name always being "" (#3317)
  • fix module section regex matching wrong things (#3321)

Modules

  • add a panel around diff previews when updating (#3246)

Subworkflows

  • Add nf-core subworkflows patch command (#2861)
  • Improve subworkflow nf-test migration warning (#3298)

General

  • Include .nf-core.yml in nf-core pipelines bump-version (#3220)
  • create: add shortcut to toggle all switches (#3226)
  • Remove unrelated values when saving .nf-core file (#3227)
  • use correct --profile options for nf-core subworkflows test (#3233)
  • Update GitHub Actions (#3237)
  • add --dir/-d option to schema commands (#3247)
  • fix headers in api docs (#3323)
  • handle new schema structure in nf-core pipelines create-params-file (#3276)
  • Update Gitpod image to use Miniforge instead of Miniconda(#3274)
  • Add hint to solve git errors with a synced repo (#3279)
  • Run pre-commit when testing linting the template pipeline (#3280)
  • Make CLI prompt less nf-core specific (#3326)
  • Update gitpod vscode extensions to use nf-core extension pack (#3327)
  • Remove toList() channel operation from inside onComplete block (#3304)
  • build: Setup VS Code tests (#3292)
  • Don't break gitpod.yml with template string (#3332)
  • rocrate: remove duplicated entries for name and version (#3333)
  • rocrate: Update crate with version bump and handle new contributor field (#3334)
  • set default_branch to master for now (#3335)
  • Set git defaultBranch to master in sync action (#3337)
  • Add verbose mode to sync action (#3339)

Version updates

  • chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 (#3230)
  • Update codecov/codecov-action action to v5 (#3283)
  • Update gitpod/workspace-base Docker digest to 12853f7 (#3309)
  • Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 (#3325)
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