Bump nf-core from 2.1 to 2.3.1

[dependabot]

Bumps nf-core from 2.1 to 2.3.1.

Release notes

Sourced from nf-core's releases.

v2.3.1 - Mercury Vulture Formatting

⚠️ TLDR: Run Prettier on your pipeline's codebase before attempting the template sync merge.

The sync PR may be a little big because of many major changes (whitespace, quotation mark styles etc). To help with the merge, we highly recommend running Prettier on your pipeline's codebase before attempting the template merge.

Please copy .editorconfig and .prettierrc.yml from the template to your pipeline root first, as they configure the behaviour of Prettier.

---

This patch release is primarily to address problems that we had in the v2.3 release with code linting. Instead of resolving those specific issues, we chose to replace the linting tools (markdownlint, yamllint) with a new tool: Prettier

This is a fairly major change and affects a lot of files. However, it will hopefully simplify future usage. Prettier can auto-format many different file formats (for pipelines the most relevant are markdown and YAML) and is extensible with plugins (Nextflow, anyone?). It tends to be a bit less strict than markdownlint and yamllint and importantly can fix files for you rather than just complaining.

To run Prettier, go to the base of the repository where .editorconfig and .prettierrc.yml are located. Make sure your git status is clean so that the changes don't affect anything you're working on and run:

prettier --write .

This runs Prettier and tells it to fix any issues it finds in place.

Please note that there are many excellent integrations for Prettier available, for example VSCode can be set up to automatically format files on save.

---

Template

• Replace markdownlint and yamllint with Prettier for linting formatting / whitespace (#1470)
• Add CI test using editorconfig-checker for other file types to look for standardised indentation and formatting (#1476)
• Add md5sum check of versions.yml to test.yml on the modules template.
• Update bundled module wrappers to latest versions (#1462)
• Renamed assets/multiqc_config.yaml to assets/multiqc_config.yml (yml not yaml) (#1471)

General

• Convert nf-core/tools API / lint test documentation to MyST (#1245)
• Build documentation for the nf-core modules lint tests (#1250)
• Fix some colours in the nf-core/tools API docs (#1467)
• Install tools inside GitPod Docker using the repo itself and not from Conda.
• Rewrite GitHub Actions workflow for publishing the GitPod Docker image.
• Improve config for PyTest so that you can run pytest instead of pytest tests/ (#1461)
• New pipeline lint test multiqc_config that checks YAML structure instead of basic file contents (#1461)
• Updates to the GitPod docker image to install the latest version of nf-core/tools

v2.3 - Mercury Vulture

Another big release that's been coming for quite some time (apologies to all who have been running with dev for weeks / months).

One or two major bugfixes, such as making nf-core download work again with the latest DSL2 formats. See below for the full list of changes in this release.

Full Changelog: nf-core/tools@2.2...2.3

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.3.1 - Mercury Vulture Formatting - [2022-03-23]

This patch release is primarily to address problems that we had in the v2.3 release with code linting. Instead of resolving those specific issues, we chose to replace the linting tools (markdownlint, yamllint) with a new tool: Prettier

This is a fairly major change and affects a lot of files. However, it will hopefully simplify future usage. Prettier can auto-format many different file formats (for pipelines the most relevant are markdown and YAML) and is extensible with plugins (Nextflow, anyone?). It tends to be a bit less strict than markdownlint and yamllint and importantly can fix files for you rather than just complaining.

The sync PR may be a little big because of many major changes (whitespace, quotation mark styles etc). To help with the merge, we highly recommend running Prettier on your pipeline's codebase before attempting the template merge. If you take this approach, please copy .editorconfig and .prettierrc.yml from the template to your pipeline root first, as they configure the behaviour of Prettier.

To run Prettier, go to the base of the repository where .editorconfig and .prettierrc.yml are located. Make sure your git status is clean so that the changes don't affect anything you're working on and run:

prettier --write .

This runs Prettier and tells it to fix any issues it finds in place.

Please note that there are many excellent integrations for Prettier available, for example VSCode can be set up to automatically format files on save.

Template

• Replace markdownlint and yamllint with Prettier for linting formatting / whitespace (#1470)
• Add CI test using editorconfig-checker for other file types to look for standardised indentation and formatting (#1476)
• Add md5sum check of versions.yml to test.yml on the modules template.
• Update bundled module wrappers to latest versions (#1462)
• Renamed assets/multiqc_config.yaml to assets/multiqc_config.yml (yml not yaml) (#1471)

General

• Convert nf-core/tools API / lint test documentation to MyST (#1245)
• Build documentation for the nf-core modules lint tests (#1250)
• Fix some colours in the nf-core/tools API docs (#1467)
• Install tools inside GitPod Docker using the repo itself and not from Conda.
• Rewrite GitHub Actions workflow for publishing the GitPod Docker image.
• Improve config for PyTest so that you can run pytest instead of pytest tests/ (#1461)
• New pipeline lint test multiqc_config that checks YAML structure instead of basic file contents (#1461)
• Updates to the GitPod docker image to install the latest version of nf-core/tools

Modules

v2.3 - Mercury Vulture - [2022-03-15]

Template

... (truncated)

Commits

• 27c98a1 Merge pull request #1483 from nf-core/dev
• ab0b99d Merge pull request #1482 from ewels/master
• 7d8ff65 Update CHANGELOG.md
• 4182507 Add Prettier instructions to the changelog
• 8c33481 Changelog, bump to 2.3.1
• 0782051 Merge pull request #1480 from projectoriented/master
• 420fe4a Merge branch 'dev' into master
• 0f4ad5c Linting again, added extra new line 🤦‍♀
• 954c5a7 Lint
• 7e50282 Update nf_core/pipeline-template/docs/usage.md
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[dependabot]

Superseded by #47.