The nf-core framework for community-curated bioinformatics pipelines.

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!

:star2: 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

:heavy_multiplication_x: 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

• 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.

• 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).

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

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

• 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)