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ENH: Add GenomeData[Proteins] and GenomeData[Loci] inputs to annotate-sample-data-amrfinderplus action #93

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VinzentRisch opened this issue Jul 18, 2024 · 1 comment

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@VinzentRisch
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The annotate-sample-data-amrfinderplus action currently only accepts contigs or MAGs as input. But The most accurate way to run amrfinderplus is to run it in a combined mode with MAGs and predicted genes together. For this the inputs for GenomeData[Proteins] and GenomeData[Loci] has to be added to the action. A user can then predict genes of their MAGs with predict-genes-prodigal of moshpit and then use those outputs to run annotate-sample-data-amrfinderplus.

@VinzentRisch
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This is currently not possible because q2-amr is only compatible with qiime2 2024.2 and the action predict-genes-prodigal of moshpit 2024.2 only accepts FeatureData[MAG].

@VinzentRisch VinzentRisch closed this as not planned Won't fix, can't repro, duplicate, stale Sep 27, 2024
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