broadinstitute / viral-core / 20919342230

71%

master: 72%

Pull #160

github

Fix sambamba index to create .bai instead of .bam.bai

Sambamba index command creates {file}.bam.bai by default, but WDL
workflows expect {file}.bai naming convention. This caused Terra
workflow failures where the task succeeded (exit code 0) but the
required .bai files were not found during output delocalization.

The fix renames the index file after creation to match the expected
naming convention for compatibility with WDL workflows.

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

16 of 18 new or added lines in 1 file covered. (88.89%)

4650 of 6569 relevant lines covered (70.79%)

0.71 hits per line