Snakemake throws MissingOutputException when a sample is completely filtered out

I thought this was accounted for, but it looks like when a sample is completely filtered out, the current workflow won't move forward

```
Read 366 items
[1] "Fri Aug 8 00:40:56 2025 Paired-end data found!"
[1] "Fri Aug 8 00:40:56 2025 Filtering..."
dqhe filter removed all reads: intermediate/ERR10127881.R1.filtered.fastq.gz and intermediate/ERR10127881.R2.filtered.fastq.gz not written.
[1] "Fri Aug 8 00:52:51 2025 Filtering complete. Saving results..."
Some input samples had no reads pass the filter.
[1] "Fri Aug 8 00:52:51 2025 Filtering results saved. Done."
Waiting at most 5 seconds for missing files.
MissingOutputException in rule filter in file /scratch/midway3/rabdill/compendium/PRJEB55648/workflow/Snakefile, line 41:
Job 0 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
```