3311 changes the behavior of csv_summary when a lingroup file is provided, limiting summarized reporting to just the named lingroups. While the output is very similar to the lingroup output we already have, the most important difference is that the sample name is included in the output, meaning that we get intelligible results when running tax metagenome on more than one sample.
Prior tax metagenome behavior was to always generate a lingroup output file when a lingroups file is provided. In #3311, we disable that for multiple queries, since the results wouldn't make sense. We do not replace it with another default, but instead add a recommendation to the help + doc.
In the next major version (5.0), we could consider changing the default lingroup output to csv_summary, since it's actually useful for multiple files. Or, we could modify the lingroup output itself to include query information.
3311 changes the behavior of csv_summary when a lingroup file is provided, limiting summarized reporting to just the named lingroups. While the output is very similar to the lingroup output we already have, the most important difference is that the sample name is included in the output, meaning that we get intelligible results when running tax metagenome on more than one sample.
Prior tax metagenome behavior was to always generate a lingroup output file when a lingroups file is provided. In #3311, we disable that for multiple queries, since the results wouldn't make sense. We do not replace it with another default, but instead add a recommendation to the help + doc.
In the next major version (5.0), we could consider changing the default lingroup output to csv_summary, since it's actually useful for multiple files. Or, we could modify the lingroup output itself to include query information.