chore(main): release 1.0.0

[varfish-bot]

🤖 I have created a release beep boop

1.0.0 (2024-10-30)

Features

• add gnomAD SV/CNV 4.0 for GRCh38 (#55) (48ba90d)
• add MinIO server for file storage purposes (#2) (#7) (34b37c4)
• add traefik service with configuration examples (#3) (#5) (8cfbc21)
• adding cadd-rest-api support via docker-compose.override.yml (#48) (c9d6c6c)
• adding ClinVar download instructions to README (#28) (d4ead82)
• adding download-data.sh script (#42) (1f6fca8)
• adding dynamic varfish data directory (#87) (fd96c82)
• adding nginx for serving track data (#15) (#20) (973b640)
• adding templates for exomiser integration (#46) (dea2c78)
• bump annonars/genes (#58) (d3cf847)
• bump downloader to be on par with reev one (#57) (a8c02e3)
• bumping annonars, clinvar data, adding clinvar-genes (#29) (fbdcaf1)
• splitting download into more steps (#75) (a6c4737)

Bug Fixes

• adding clinvar links for mehari (#83) (dbb254a)
• adding hgnc_xlink.tsv for viguno (#79) (6929e71)
• adding s3:GetBucketLocation to minio policy (#30) (9e94ad0)
• adding segdup besides old seqdup (#84) (18ad21d)
• adding viguno env setup (c5c759a)
• adjust downloads for worker and mehari (#80) (0f479c5)
• allow graceful shutdown of minio-client container (#21) (575c07e)
• bump mehari-data-tx to 0.6.0 (#59) (3ffacf9)
• bump version in annonars genes (8ab9538)
• docker-compose.override.yml file for certificate (#72) (a076d3f)
• docker-compose.override.yml for cadd-rest-api (#73) (ce3a7df)
• Fix download script variable names (#61) (73d88db)
• mehari freqs path (#70) (6fb8dcb)
• putting BOT_TOKEN into release-please GitHub actions workflow (#68) (049d3df)
• seqdup => segdup (083c66f)
• typo mime2gene (#85) (70e3854)
• update readme (#41) (7b53228)
• updating cadd-rest-api.env example file (#50) (81eeb8a)
• using bitnami minio clients to startup works again (#36) (7e199f3)
• various version changes (#82) (fd050b9)

---

This PR was generated with Release Please. See documentation.

Summary by CodeRabbit

• New Features

  • Added gnomAD SV/CNV version 4.0 for GRCh38.
  • Introduced a MinIO server for file storage and integrated Nginx for serving track data.
  • Updated README with ClinVar download instructions and added a new script for data downloads.
  • Included templates for Exomiser integration and support for cadd-rest-api.

• Bug Fixes

  • Fixed various links and paths related to the Mehari and Viguno projects.
  • Updated policies and configurations for MinIO and Docker services.
  • Corrected variable names in the download script and made minor documentation updates.

[coderabbitai]

Walkthrough

The changes in this pull request primarily involve updates to the CHANGELOG.md file for version 1.0.0, dated 2024-10-30. This includes the addition of new features such as gnomAD SV/CNV version 4.0, a MinIO server for file storage, and a Traefik service. Bug fixes include updates to ClinVar links, the addition of necessary files for projects, and various improvements to the download process and environment setup. Additionally, dependency versions have been bumped, and minor corrections have been made throughout the documentation.

Changes

File/Path	Change Summary
CHANGELOG.md	Updated for version 1.0.0, dated 2024-10-30, detailing new features and bug fixes.
docker-compose.override.yml	Added support for cadd-rest-api and updated for certificates.
README.md	Updated with ClinVar download instructions and minor typo fixes.
download-data.sh	New script added; variable names corrected.
Various project files	Added ClinVar links for Mehari, hgnc_xlink.tsv for Viguno, and updated MinIO policy.
Dependencies	Bumped versions for annonars/genes, downloader, and mehari-data-tx to 0.6.0.

Poem

In the garden where data blooms,
A MinIO server dispels the glooms.
With Traefik's guidance, we sail so free,
While gnomAD's treasures await for thee.
Bugs are fixed, and scripts are new,
Hopping along, we celebrate too! 🐇✨

---

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• CHANGELOG.md (1 hunks)

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• CHANGELOG.md

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[coderabbitai]

Actionable comments posted: 1

🧹 Outside diff range and nitpick comments (2)

CHANGELOG.md (2)

6-20: Consider grouping features by theme for better readability.

While the feature entries are well-documented with proper issue linking, consider organizing them into thematic groups such as:

• Infrastructure (MinIO, traefik, nginx)
• Data Sources (gnomAD, ClinVar)
• Tooling (download scripts, templates)
• Dependencies (version bumps)

---

22-43: Enhance bug fix descriptions with impact context.

Consider adding brief impact descriptions to bug fixes. For example:

• "adding s3:GetBucketLocation to minio policy" could be "fix: add s3:GetBucketLocation to MinIO policy to resolve bucket access issues"
• "seqdup => segdup" could be "fix: correct seqdup to segdup naming for consistency with upstream changes"

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🧰 Additional context used

🔇 Additional comments (1)

CHANGELOG.md (1)

1-5: LGTM! Header follows changelog best practices.

The version header is properly formatted with semantic versioning and ISO 8601 date format.

[coderabbitai]

⚠️ Potential issue

Remove duplicate Changelog header.

The "## Changelog" header at line 45 appears to be a duplicate of the main header and should be removed.

-## Changelog

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

## Changelog