Nf-core

Template

- Remove obsolete editor settings in `devcontainer.json` and `gitpod.yml` ([2795](https://github.com/nf-core/tools/pull/2795))
- Add nf-test test instructions to contributing and PR template ([2807](https://github.com/nf-core/tools/pull/2807))
- Fix topic extraction step for hashtags in toots ([2810](https://github.com/nf-core/tools/pull/2810))
- Update modules and subworkflows in the template ([2811](https://github.com/nf-core/tools/pull/2811))
- Unpin setup-nextflow and action-tower-launch ([2806](https://github.com/nf-core/tools/pull/2806))

Download

- Improved offline container image resolution by introducing symlinks, fixes issues [2751](https://github.com/nf-core/tools/issues/2751), [#2644](https://github.com/nf-core/tools/issues/2644) and [demultiplex#164](https://github.com/nf-core/demultiplex/issues/164): ([#2768](https://github.com/nf-core/tools/pull/2768))

Linting

Components

General

- chore(deps): update codecov/codecov-action digest to 0cfda1d ([2794](https://github.com/nf-core/tools/pull/2794))
- chore(deps): update gitpod/workspace-base docker digest to c15ee2f ([2799](https://github.com/nf-core/tools/pull/2799))

Template

- Add empty line in README.md to fix badges. ([2729](https://github.com/nf-core/tools/pull/2729))
- Replace automatic branch detection in `nf-core download` CI test with hardcoded `dev` and input. ([2727](https://github.com/nf-core/tools/pull/2727))
- Add Github Action to automatically cleanup ubuntu-latest runners to fix runner running out of diskspace errors([2755](https://github.com/nf-core/tools/issues/2755))
- Fix GitHub Actions CI and Linting badges links ([2757](https://github.com/nf-core/tools/pull/2757))
- Add hashtags to release announcement on mastodon ([2761](https://github.com/nf-core/tools/pull/2761))
- update fastqc and multiqc in template ([2776](https://github.com/nf-core/tools/pull/2776))
- template refactoring: remove the `lib` directory and use nf-core subworkflows ([2736](https://github.com/nf-core/tools/pull/2736))
- use nf-validation to create an input channel from a sample sheet ([2736](https://github.com/nf-core/tools/pull/2736))

Linting

- Make creat-lint-wf composable ([2733](https://github.com/nf-core/tools/pull/2733))
- Add looser comparison when pipeline logos ([2744](https://github.com/nf-core/tools/pull/2744))
- Handle multiple aliases in module imports correctly during linting ([2762](https://github.com/nf-core/tools/pull/2762))
- Switch to markdown based API and error docs ([2758](https://github.com/nf-core/tools/pull/2758))

Modules

- Handle dirty local module repos by force checkout of commits and branches if needed ([2734](https://github.com/nf-core/tools/pull/2734))
- Patch: handle file not found when it is an added file to a module ([2771](https://github.com/nf-core/tools/pull/2771))
- Handle symlinks when migrating pytest ([2770](https://github.com/nf-core/tools/pull/2770))
- Add `--profile` parameter to nf-test command ([2767](https://github.com/nf-core/tools/pull/2767))

General

- fix ignoring changes in partially templated files (e.g. `.gitignore`) ([2722](https://github.com/nf-core/tools/pull/2722))
- update ruff to 0.2.0 and add it to pre-commit step ([2725](https://github.com/nf-core/tools/pull/2725))
- Update codecov/codecov-action digest to e0b68c6 ([2728](https://github.com/nf-core/tools/pull/2728))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1 ([2730](https://github.com/nf-core/tools/pull/2730))
- Update python:3.11-slim Docker digest to 2a746e2 ([2743](https://github.com/nf-core/tools/pull/2743))
- Update actions/setup-python action to v5 ([2739](https://github.com/nf-core/tools/pull/2739))
- Update gitpod/workspace-base Docker digest to 45e7617 ([2747](https://github.com/nf-core/tools/pull/2747))
- chore(deps): pin jlumbroso/free-disk-space action to 54081f1 ([2756](https://github.com/nf-core/tools/pull/2756))
- chore(deps): update actions/github-script action to v7 ([2766](https://github.com/nf-core/tools/pull/2766))
- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.2.2 ([2769](https://github.com/nf-core/tools/pull/2769))
- Update gitpod/workspace-base Docker digest to 728e1fa ([2780](https://github.com/nf-core/tools/pull/2780))

Linting

- Handle default values of type number from nextflow schema ([2703](https://github.com/nf-core/tools/pull/2703))
- fix ignoring files_unchanged ([2707](https://github.com/nf-core/tools/pull/2707))

General

- Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15 ([2705](https://github.com/nf-core/tools/pull/2705))
- use types for default value comparison ([2712](https://github.com/nf-core/tools/pull/2712))
- fix changelog titles ([2708](https://github.com/nf-core/tools/pull/2708))
- Print relative path not absolute path in logo cmd log output ([2709](https://github.com/nf-core/tools/pull/2709))
- Update codecov/codecov-action action to v4 ([2713](https://github.com/nf-core/tools/pull/2713))
- Ignore nf-core-bot in renovate PRs ([2716](https://github.com/nf-core/tools/pull/2716))

Template

- Add a Github Action Workflow to the pipeline template that tests a successful download with `nf-core download` ([2618](https://github.com/nf-core/tools/pull/2618))
- Use `pre-commit` to lint files in GitHub CI ([2635](https://github.com/nf-core/tools/pull/2635))
- Use pdiff also on gitpod for nf-test ([2640](https://github.com/nf-core/tools/pull/2640))
- switch to new image syntax in readme ([2645](https://github.com/nf-core/tools/pull/2645))
- Add conda channel order to nextflow.config ([2094](https://github.com/nf-core/tools/pull/2094))
- Fix tyop in pipeline nextflow.config ([2664](https://github.com/nf-core/tools/pull/2664))
- Remove `nfcore_external_java_deps.jar` from lib directory in pipeline template ([2675](https://github.com/nf-core/tools/pull/2675))
- Add function to check `-profile` is well formatted ([2678](https://github.com/nf-core/tools/pull/2678))
- Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message ([2680](https://github.com/nf-core/tools/pull/2680))
- add 👀👍🏻🎉😕 reactions to fix-linting-bot action ([2692](https://github.com/nf-core/tools/pull/2692))

Linting

- Fix linting of a pipeline with patched custom module ([2669](https://github.com/nf-core/tools/pull/2669))
- linting a pipeline also lints the installed subworkflows ([2677](https://github.com/nf-core/tools/pull/2677))
- environment.yml name must be lowercase ([2676](https://github.com/nf-core/tools/pull/2676))
- allow ignoring specific files when template_strings ([2686](https://github.com/nf-core/tools/pull/2686))
- lint `nextflow.config` default values match the ones specified in `nextflow_schema.json` ([2684](https://github.com/nf-core/tools/pull/2684))

Modules

- Fix empty json output for `nf-core list local` ([2668](https://github.com/nf-core/tools/pull/2668))

General

- Run CI-pytests for nf-core tools on self-hosted runners ([2550](https://github.com/nf-core/tools/pull/2550))
- Add Ruff linter and formatter replacing Black, isort and pyupgrade ([2620](https://github.com/nf-core/tools/pull/2620))
- Set pdiff as nf-test differ in Docker image for Gitpod ([2642](https://github.com/nf-core/tools/pull/2642))
- Fix Renovate Dockerfile updating issues ([2648](https://github.com/nf-core/tools/pull/2648) and [#2651](https://github.com/nf-core/tools/pull/2651))
- Add new subcommand `nf-core tui`, which launches a TUI (terminal user interface) to intuitively explore the command line flags, built using [Trogon](https://github.com/Textualize/trogon) ([#2655](https://github.com/nf-core/tools/pull/2655))
- Add new subcommand: `nf-core logo-create` to output an nf-core logo for a pipeline (instead of going through the website) ([2662](https://github.com/nf-core/tools/pull/2662))
- Handle api redirects from the old site ([2672](https://github.com/nf-core/tools/pull/2672))
- Remove redundanct v in pipeline version for emails ([2667](https://github.com/nf-core/tools/pull/2667))
- add function to check `-profile` is well formatted ([2678](https://github.com/nf-core/tools/pull/2678))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.14 ([2674](https://github.com/nf-core/tools/pull/2674))
- Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([2630](https://github.com/nf-core/tools/pull/2630))
- Update mshick/add-pr-comment action to v2 ([2632](https://github.com/nf-core/tools/pull/2632))
- update python image version in docker file ([2636](https://github.com/nf-core/tools/pull/2636))
- Update actions/cache action to v4 ([2666](https://github.com/nf-core/tools/pull/2666))
- Update peter-evans/create-or-update-comment action to v4 ([2683](https://github.com/nf-core/tools/pull/2683))
- Update peter-evans/create-or-update-comment action to v4 ([2695](https://github.com/nf-core/tools/pull/2695))

Template

- Rename `release-announcments.yml` to `release-announcements.yml` ([2610](https://github.com/nf-core/tools/pull/2610))
- Fix `nextflow.config` `docker.runOptions` ([2607](https://github.com/nf-core/tools/pull/2607))

General

- Only dump `modules.json` when it is modified ([2609](https://github.com/nf-core/tools/pull/2609))

Template

- Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([2465](https://github.com/nf-core/tools/pull/2465))
- Fancier syntax highlighting for example samplesheets in the usage.md template ([2503](https://github.com/nf-core/tools/pull/2503))
- Use closure for multiqc ext.args ([2509](https://github.com/nf-core/tools/pull/2509))
- Fix how the modules template references the conda environment file ([2540](https://github.com/nf-core/tools/pull/2540))
- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([2569](https://github.com/nf-core/tools/pull/2569))
- Pin the version of nf-validation ([2579](https://github.com/nf-core/tools/pull/2579))
- Disable process selector warnings by default ([2161](https://github.com/nf-core/tools/issues/2161))
- Remove `docker.userEmulation` from nextflow.config in pipeline template ([2580](https://github.com/nf-core/tools/pull/2580))

Download

- Add `docker://` prefix for absolute container URIs as well ([2576](https://github.com/nf-core/tools/pull/2576)).
- Bugfix for AttributeError: `ContainerError` object has no attribute `absoluteURI` ([2543](https://github.com/nf-core/tools/pull/2543)).

Linting

- Fix incorrectly failing linting if 'modules' was not found in meta.yml ([2447](https://github.com/nf-core/tools/pull/2447))
- Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([2448](https://github.com/nf-core/tools/pull/2448))
- Add pyupgrade to pre-commit config and dev requirements as mentioned in [2200](https://github.com/nf-core/tools/issues/2200)
- Check for spaces in modules container URLs ([2452](https://github.com/nf-core/tools/issues/2452))
- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables when linting a pipeline. ([2507](https://github.com/nf-core/tools/pull/2507))
- Lint nf-test main.nf.test tags include all used components in chained tests ([2572](https://github.com/nf-core/tools/pull/2572))
- Don't fail linting if md5sum for empty files are found in a stub test ([2571](https://github.com/nf-core/tools/pull/2571))
- Check for existence of test profile ([2478](https://github.com/nf-core/tools/pull/2478))

Modules

- Added stub test creation to `create_test_yml` ([2476](https://github.com/nf-core/tools/pull/2476))
- Replace ModulePatch by ComponentPatch ([2482](https://github.com/nf-core/tools/pull/2482))
- Fixed `nf-core modules lint` to work with new module structure for nf-test ([2494](https://github.com/nf-core/tools/pull/2494))
- Add option `--migrate-pytest` to create a module with nf-test taking into account an existing module ([2549](https://github.com/nf-core/tools/pull/2549))
- When installing modules and subworkflows, automatically create the `./modules` directory if it doesn't exist ([2563](https://github.com/nf-core/tools/issues/2563))
- When `.nf-core.yml` is not found create it in the current directory instead of the root filesystem ([2237](https://github.com/nf-core/tools/issues/2237))
- Modules `--migrate-pytest` copies template scripts ([2568](https://github.com/nf-core/tools/pull/2568))

Subworkflows

- Added stub test creation to `create_test_yml` ([2476](https://github.com/nf-core/tools/pull/2476))
- Fixed `nf-core subworkflows lint` to work with new module structure for nf-test ([2494](https://github.com/nf-core/tools/pull/2494))
- Add option `--migrate-pytest` to create a subworkflow with nf-test taking into account an existing subworkflow ([2549](https://github.com/nf-core/tools/pull/2549))

General

- Update `schema build` functionality to automatically update defaults which have changed in the `nextflow.config`([2479](https://github.com/nf-core/tools/pull/2479))
- Change testing framework for modules and subworkflows from pytest to nf-test ([2490](https://github.com/nf-core/tools/pull/2490))
- `bump_version` keeps now the indentation level of the updated version entries ([2514](https://github.com/nf-core/tools/pull/2514))
- Add mypy to pre-commit config for the tools repo ([2545](https://github.com/nf-core/tools/pull/2545))
- Use Path objects for ComponentCreate and update the structure of components templates ([2551](https://github.com/nf-core/tools/pull/2551)).
- GitPod base image: swap tool installation back to `conda` from `mamba` ([2566](https://github.com/nf-core/tools/pull/2566)).
- Sort the `installed_by` list in `modules.json` ([2570](https://github.com/nf-core/tools/pull/2570)).
- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([2569](https://github.com/nf-core/tools/pull/2569))