Using MultiQC with kallisto

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Hello, I am trying to create a simple bulk RNAseq workflow with kallisto pseudoalignment. Everything works except for aggregation of QC results with multiQC using kallisto outputs (STAR works fine).

Error: Module 'kallisto: ‘finding pseudoalignments for the reads’ not found in the file ‘SRR9126659’

I read here that for QC metrics one must save logs from kallisto in a separate file log file from Kallisto · Issue #440 · MultiQC/MultiQC · GitHub

Is there a way to access these logs in Galaxy for further use? Or generally get QC metrics on kallisto using Galaxy?

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Welcome, @GeorgiiVdovin

Thanks for bringing this up! We know about the special use, and didn’t have a specific issue ticket for this yet. I’ve created that here.

Please feel free to add more details if you would like to. And, if that is something you would like to help with, that ticket is the place to get started – just state so and the IUC will guide you. This doesn’t seem overly complicated and we have other tools you could model this on (HISAT2’s alignment summary is one example).

Thanks and please let me know if I have misunderstood anything! :slight_smile: