When all samples have less than params.lowread_filter reads, the pipeline errors at qiime_datamerge step. The ideal behavior should be the pipeline still finishes and produces report, but with a message on the comment section of the report, similar to how bad samples are handled right row.
In a related note, when samples produce sourmash results, but the results are completely filtered out by strict filtering criteria, the sourmash_qiimeprep process produces empty files for qiime to import.
When all samples have less than
params.lowread_filter
reads, the pipeline errors at qiime_datamerge step. The ideal behavior should be the pipeline still finishes and produces report, but with a message on the comment section of the report, similar to how bad samples are handled right row.