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@mirpedrol mirpedrol released this 25 Sep 14:44
· 1755 commits to master since this release
2.10
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v2.10 - Nickel Ostrich + [2023-09-25]

This new release includes new commands, template updates, and several bug fixes. Thanks to all contributors for making this possible!

🌟 Highlights

  • We are now linting subworkflows nf-core subworkflows lint.
  • Use nf-core create-params-file params-file with documentation and default values for all parameters in a pipeline.
  • A new GitHub Action will automatically post new pipeline release messages to Mastodon, Bluesky and Twitter
  • Pipelines in sync with the new template, will dump all pipeline parameters to a file called params.json after every run

✖️ Deprecations

  • Deprecation of the —no-git argument for nf-core create command
  • Deprecation of the —template-yaml argument for the nf-core sync command - The same information will now be automatically stored in .nf-core.yml

Template

  • Fix links in multiqc_config.yml (#2372 and #2412)
  • Remove default false from nextflow_schema.json (#2376)
  • Add module MULTIQC to modules.config (#2377)
  • Add GitHub workflow for automated release announcements (#2382)
  • Update the Code of Conduct (#2381)
  • Save template information to .nf-core.yml and deprecate argument --template-yaml for nf-core sync (#2388 and #2389)
  • (#2397) Remove fixed Ubuntu test and added to standard testing matrix
  • (#2396) Reduce container finding error to warning since the registries are not consistent.
  • (#2415) Add autoMounts for apptainer.
  • Remove igenomes_base from the schema, so that nf-validation doesn't create a file path and throw errors offline for s3 objects.
  • Modified devcontainer permissions so that singularity can be run in Codespaces/VS Code devcontainers (Commit a103f44)
  • Update Gitpod profile resources to reflect base environment settings.
  • (#747) Add to the template the code to dump the selected pipeline parameters into a json file.

Download

  • Improved container image resolution and prioritization of http downloads over Docker URIs (#2364).
  • Registries provided with -l/--container-library will be ignored for modules with explicit container registry specifications (#2403).
  • Fix unintentional downloading of containers in test for the Tower download functionality. Bug reported by @adamrtalbot and @awgymer (#2434).

Linting

  • Add new command nf-core subworkflows lint (#2379)

Modules

Subworkflows

  • Fix bug: missing subworkflow name when using nf-core subworkflows create (#2435)

General

  • Initialise docker_image_name to fix UnboundLocalError error (#2374)
  • Fix prompt pipeline revision during launch (#2375)
  • Add a create-params-file command to create a YAML parameter file for a pipeline containing parameter documentation and defaults. (#2362)
  • Update the Code of Conduct (#2381)
  • Remove --no-git option from nf-core create (#2394)
  • Throw warning when custom workflow name contains special characters (#2401)
  • Bump version of nf-test snapshot files with nf-core bump-version (#2410)

Contributors

adamrtalbot and awgymer
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