Exit code when no marker gene was found

EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes

GNU General Public License v3.0

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Exit code when no marker gene was found #12

Open openpaul opened 3 years ago

openpaul commented 3 years ago

EukCC currently behaves unexpected when no marker gene was found or it could not place the bin in the tree.

Suggested behaviour:

Give log message that nothing could be done.
Output eukcc.tsv file with NA for completeness and contamination.
Give exit code 0

madscort commented 1 year ago

Thanks a lot for your work. This would be a valuable improvement. When working with eukCC in a workflow handling multiple samples and multiple bins, it is expected and fine to have many bins not giving any results. In the current version it is difficult to automate the results handling, since the program gives the same non-zero exit code for no results and a program failure. The solution given above would be perfect.