broadinstitute / viral-core / 20554005305

70%

master: 70%

Pull #153

github

Fix rmdup_mvicuna_bam silently swallowing mvicuna failures

When mvicuna fails (e.g., OOM killed with SIGKILL), the exception was
caught and logged but not re-raised. This caused the function to continue
executing, producing an empty output BAM file (0 reads) while returning
success (exit code 0).

Now the exception is re-raised after logging, ensuring the workflow
properly fails when mvicuna encounters an error.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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