🔨📝 Non Prod Plink and Doc Updates

Non-prod tools added and documentation updated for clarity for small cohort joint genotyping workflow, including the following points:

• It is a small cohort calling workflow, not a study-wide one, intended for trios mostly
• It also follows best practices for WGS. WXS will follow in a later update
• Documentation now describes workflow outputs

What's Changed

• ✨ add plink tools and wf by @dmiller15 in #42
• Plink Adjustments from Cohort Running by @dmiller15 in #43
• 📚 update GCP ref link by @dmiller15 in #44
• 🤖 add docker table builder by @dmiller15 in #45
• 📚 update gatk doc links by @dmiller15 in #46
• 📝 update docs by @migbro in #47

Full Changelog: v2.4.0...v2.4.1

💫 Refactor Annotation

To meet new standards:

• CADD, InterVar, dbnsfp, ClinVar dropped as default/recommended annotations. They are now optional
• gnomAD v3.1.1 annotation now done by ecthvar with custom fields added (see README here)
• Germline git submodule replaced with more focused kf-annotation-tools

What's Changed

• 💫 Refactor Annotation by @migbro in #41

Full Changelog: v2.3.2...v2.4.0

📖 Updated Default Cavatica Refs

After exporting our default refs to a bucket, cavatica pointers were updated. Functionality of the app is not affected, except on cavatica, using an old version risks a couple files not being pulled in automatically.
Also upgraded submodule pointer to ensure correct version is being used compatible with the update.

What's Changed

• 📖 Changed default reference location after export by @migbro in #39

Full Changelog: v2.3.1...v2.3.2

✏️ Set new default for tool name

To match the standard established by the single sample genotyping workflow, to satisfy ops harmonization requirements, we are updating the default file extension.

What's Changed

• 🔧 Update default File Prefix by @migbro in #38

Full Changelog: v2.3.0...v2.3.1

💪 DNA Annotation Upgrade

This release is part of the overall effort to harmonize annotation sources used across all pipelines.
Following the path of the single sample genotyping workflow:

• Added standalone wf with ability to strip old annotations to avoid conflicts and re-use old calls
• Upgraded from VEP 93 to VEP 105
• Incorporated workflow into single sample calling
• Added updated gnomad, clinvar, and dbsnsfp and intervar references to enhance "off-the-shelf" usability for downstream germline users

What's Changed

• 🚀 DNA Annotation Upgrade by @migbro in #37

Full Changelog: v2.2.3...v2.3.0

KFDRC Genotyping Production Workflow

What's Changed

• ⚡ Improve Resource Usage by @dmiller15 in #36

Full Changelog: v2.2.2...v2.2.3

KFDRC Genotyping Production Workflow

Bug fix for suggested file ids.

KFDRC Genotyping Production Workflow

This release updates the docker being pulled for peddy from using latest to being pinned to peddy v0.4.2. This is functionally equivalent to v2.2.0.

KFDRC Genotyping Production Workflow

This release updates the dockerPulls for all tools that were using a DockerHub registry.

KFDRC Genotyping Production Workflow

This release fixes a bug in the public app where files were pointing to non-public file ID's.