fix: finish pathoscope cleanly when no candidate OTUs are found#197
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igboyes merged 1 commit intoJul 2, 2026
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A sample with no reads mapping to any default isolate produces an empty isolate FASTA. bowtie2-build exits 1 on empty input, crashing the job. Guard on intermediate.lengths so build_isolate_index skips the index build, map_isolates and eliminate_subtraction short-circuit, and reassignment uploads an empty result. The analysis now finishes as a valid negative result instead of failing. Fixes WORKFLOWS-BB
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Summary
bowtie2-buildexits 1 on empty input, crashing the workflow (VIR-2569 / SentryWORKFLOWS-BB).intermediate.lengths:build_isolate_indexskips the index build,map_isolatesandeliminate_subtractionshort-circuit, andreassignmentuploads an empty result — the analysis now finishes as a valid negative result instead of failing.intermediate.lengthscontract.Fixes WORKFLOWS-BB