broadinstitute / viral-assemble / 20761831555

69%

master: 68%

Pull #65

github

Write header-only output when skani produces no matches

When skani dist finds no matches and produces an empty file (0 bytes),
the downstream code fails because readFlatFileHeader returns [''] for
an empty file, causing issues with csv.DictWriter. This fixes the
SIGPIPE (exit code 141) that occurs in Terra/Cromwell workflows.

The fix ensures that when the input file is empty, we write a proper
header-only TSV file instead of an empty file. This allows downstream
code to properly parse the header and handle the no-matches case.

Also refactors the skani dist header into a module-level constant
(SKANI_DIST_HEADER) to avoid duplication.

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

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

239 of 379 branches covered (63.06%)

Branch coverage included in aggregate %.

1433 of 2035 relevant lines covered (70.42%)

0.7 hits per line