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Describe the problem or feature in addition to a link to the issues.

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@a-frantz
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a-frantz commented Sep 17, 2025

this comment will be updated with the pass/fail of our tools as I test

arriba.wdl: rejects empty BAM (ERROR: no normal reads found) 🎉 although it's fine with malformed RGs
bwa.wdl: all tasks "succeed" on empty FASTQs
deeptools.wdl: works with bad RGs. Empty BAM causes divide by zero error
fastp.wdl: accepts empty FASTQs
fastqc.wdl: works with bad RGs and empty BAMs
fq.wdl: lint accepts empty FQs, subsample with a probability works but a record_count=1 causes a panic
gatk4.wdl: skipped
htseq.wdl: count accepted an empty BAM
kraken2.wdl: output contains -nan where numbers should be, but exits with a 0
librarian.wdl: task fails and a helpful error is reported to STDOUT (nothing to STDERR)
mosdepth: coverage exits 0, but output summary is well formed with 0s across the board

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