BALSAMIC
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feat: replace vardict with tnscope
Description
This PR is a branch of: deduplicate_with_umi (https://github.com/Clinical-Genomics/BALSAMIC/pull/1358) Which is a branch of: Update sentieon: (https://github.com/Clinical-Genomics/BALSAMIC/tree/update_sentieon)
This PR replaces VarDict with TNscope and cleans up the snakemake rules a bit in general, such as removing the rules for TNhaplotyper which has not been in use for a long time.
For now it also removes the ML-model in TNscope since there is currently no available ML model supported for the new version of Sentieon. They are working on making a new model.
Added
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Changed
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Fixed
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Removed
- ML-model for TNscope is removed due to license issue with new version of Sentieon
Documentation
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- [ ] Updated Balsamic documentation to reflect the changes as needed for this PR.
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Tests
Feature Tests
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Pipeline Integrity Tests
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Report deliver (generation of the
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TGA T/O Workflow
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UMI T/O Workflow
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UMI T/N Workflow
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PON Workflow
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Clinical Genomics Stockholm
Documentation
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Atlas documentation
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Web portal for Clinical Genomics
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User Changes
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- [ ] This PR affects the output files or results.
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Infrastructure Changes
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Stored files in Housekeeper
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CG (CLI and delivered/uploaded files)
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Servers (configuration files on Hasta)
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Scout interface
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Checklist
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Ensure that all checkboxes below are ticked before merging.
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