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bio-raum / FooDMe2

A nextflow pipeline for the identification of species from mixed samples based on mitochondrial amplicons
https://bio-raum.github.io/FooDMe2/
GNU General Public License v3.0
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🐛 [BUG] - Benchmarking evaluates predicted taxa below the expected taxa as FP #75

Open gregdenay opened 3 days ago

gregdenay commented 3 days ago

Description

In cases where the predicted taxa are at rank below the expected taxa, this will be predicted as FP. For example in the foodme1 dataset, kangaroos are given at the familly ranks because the species are not known, predicting Macropus giganteus is evaluated as FP. This would also be the case on the rare occurence of predicting organisms to the sub-species level.

Correct behaviour should be that they are evaluated as TP.

Nextflow version

24.04.4

Pipeline version

1.0.0

Reproduction steps

nextflow run bio-raum/FooDMe2 \
  -profile conda,dobrovolny_benchmark \
  -r main

Logs

No response

Deployment

Conda/Mamba

OS

Linux

gregdenay commented 2 days ago

Also the TN results are effectively not appearing in the excel table. It would be useful to still have them in the results in order to check the filtering threshold.