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@iamh2o iamh2o commented Aug 21, 2025

Summary

  • add AIVariant SNV caller rules to process tumor-normal pairs
  • configure AIVariant parameters in local and slurm profiles
  • track tumor-normal pairs in rule_common and expose chromosome chunks
  • use tum_nrm_sampleid_match column for pairing instead of external_sample_id
  • update sample manifests, schema, and manifest generation scripts for the new column

Testing

  • snakemake --lint (fails: command not found)
  • pytest

https://chatgpt.com/codex/tasks/task_e_68a2db7ec2f083319644519f7e8c8e42

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