Nf-core

Template

- Remove automated release tweets ([3419](https://github.com/nf-core/tools/pull/3419))
- Update template components ([3426](https://github.com/nf-core/tools/pull/3426))
- Fix `process.shell` in `nextflow.config` ([3416](https://github.com/nf-core/tools/pull/3416)) and split into new lines ([#3425](https://github.com/nf-core/tools/pull/3425))

Modules

- Modules created in pipelines "local" dir now use the full template ([3256](https://github.com/nf-core/tools/pull/3256))

Subworkflows

- Subworkflows created in pipelines "local" dir now use the full template ([3256](https://github.com/nf-core/tools/pull/3256))

General

- Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.1.2 ([3414](https://github.com/nf-core/tools/pull/3414))
- Update python:3.12-slim Docker digest to 123be56 ([3421](https://github.com/nf-core/tools/pull/3421))

Template

- Bump nf-schema to `2.3.0` ([3401](https://github.com/nf-core/tools/pull/3401))
- Remove jinja formatting which was deleting line breaks ([3405](https://github.com/nf-core/tools/pull/3405))

Download

- Allow `nf-core pipelines download -r` to download commits ([3374](https://github.com/nf-core/tools/pull/3374))
- Fix faulty Download Test Action to ensure that setup and test run as one job and on the same runner ([3389](https://github.com/nf-core/tools/pull/3389))

Modules

- Fix bump-versions: only append module name if it is a dir and contains `main.nf` ([3384](https://github.com/nf-core/tools/pull/3384))

General

- `manifest.author` is not required anymore ([3397](https://github.com/nf-core/tools/pull/3397))
- Parameters schema validation: allow `oneOf`, `anyOf` and `allOf` with `required` ([3386](https://github.com/nf-core/tools/pull/3386))
- Run pre-comit when rendering template for pipelines sync ([3371](https://github.com/nf-core/tools/pull/3371))
- Fix sync GHA by removing quotes from parsed branch name ([3394](https://github.com/nf-core/tools/pull/3394))

Template

- Use outputs instead of the environment to pass around values between steps in the Download Test Action ([3351](https://github.com/nf-core/tools/pull/3351))
- Fix pre commit template ([3358](https://github.com/nf-core/tools/pull/3358))
- Set LICENSE copyright to nf-core community ([3366](https://github.com/nf-core/tools/pull/3366))
- fix including modules.config ([3356](https://github.com/nf-core/tools/pull/3356))

Linting

- Linting of pipeline LICENSE file is a warning to allow for author/maintainer names ([3366](https://github.com/nf-core/tools/pull/3366))

General

- Add missing p ([3357](https://github.com/nf-core/tools/pull/3357))
- Use `manifest.contributors` names if available, otherwise default to `manifest.author` ([3362](https://github.com/nf-core/tools/pull/3362))
- Properly parse the names form `manifest.contributors` ([3364](https://github.com/nf-core/tools/pull/3364))

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

Download

- First steps towards fixing [3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity `https://` Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)).
- Further steps towards fixing [3179](https://github.com/nf-core/tools/issues/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](https://github.com/nf-core/tools/pull/3293)).
- Update dawidd6/action-download-artifact action to v7 ([3306](https://github.com/nf-core/tools/pull/3306))

Linting

- allow mixed `str` and `dict` entries in lint config ([3228](https://github.com/nf-core/tools/pull/3228))
- fix `meta_yml` linting test failing due to `module.process_name` always being `""` ([3317](https://github.com/nf-core/tools/pull/3317))
- fix module section regex matching wrong things ([3321](https://github.com/nf-core/tools/pull/3321))

Modules

- add a panel around diff previews when updating ([3246](https://github.com/nf-core/tools/pull/3246))

Subworkflows

- Add `nf-core subworkflows patch` command ([2861](https://github.com/nf-core/tools/pull/2861))
- Improve subworkflow nf-test migration warning ([3298](https://github.com/nf-core/tools/pull/3298))

General

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

Version updates

- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([3230](https://github.com/nf-core/tools/pull/3230))
- Update codecov/codecov-action action to v5 ([3283](https://github.com/nf-core/tools/pull/3283))
- Update gitpod/workspace-base Docker digest to 12853f7 ([3309](https://github.com/nf-core/tools/pull/3309))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 ([3325](https://github.com/nf-core/tools/pull/3325))

Template

- Add null/ to .gitignore ([3191](https://github.com/nf-core/tools/pull/3191))
- Parallelize pipeline GHA tests over docker/conda/singularity ([3214](https://github.com/nf-core/tools/pull/3214))
- Fix `template_version_comment.yml` github action ([3212](https://github.com/nf-core/tools/pull/3212))
- Fix pre-commit linting on pipeline template ([3218](https://github.com/nf-core/tools/pull/3218))

Linting

- Fix bug when linting schema params and when using `defaultIgnoreParams` ([3213](https://github.com/nf-core/tools/pull/3213))

General

- Use updated pipeline commands in docstrings ([3215](https://github.com/nf-core/tools/pull/3215))
- Disable automatic sync on release, fix handling empty pipeline input ([3217](https://github.com/nf-core/tools/pull/3217))

Template

- Fixed an issue where the linting CI action didn't read the correct file ([3202](https://github.com/nf-core/tools/pull/3202))
- Fixed condition for `awsfulltest` to run ([3203](https://github.com/nf-core/tools/pull/3203))
- Fix too many empty lines added by jinja ([3204](https://github.com/nf-core/tools/pull/3204) and [#3206](https://github.com/nf-core/tools/pull/3206))
- Fix header blocks in local subworkflow including git merge marker-like strings ([3201](https://github.com/nf-core/tools/pull/3201))
- Update included subworkflows and modules ([3208](https://github.com/nf-core/tools/pull/3208))