Fix civic database update

• update civic docker image to make civic not dependent on database update
• add pharmagkt
• minor fix

GATK latest version and minor updates

GATK to v4.5.0.0
new parameters: transcript list, splicing window size
new filtering strategy: keep all pathogenic variants irrespective of other parameters such as variant classification
minor bug fix

Introduce civic, alpha missense, update database to nov 2023

♻️ Refactor code to accomodate patient based annotation, add filter module
✨ Add civic, alphamissense annotation
🗃️ Update all database up to november 2023
📚 Update docs
🚑 Fix small bugs

Workaround funcotator bug

1. add workaround to funcotator bug in gencode failure
2. improve documentation
3. improve biomarker pipelines

v1.1

1. Introduce nfcore schema
2. introduce single samplesheet input

v1.0

Official release of variantalker v1.0