Welcome @Milos
We tend to avoid offering scientific guidance at this forum since field specialist are usually not available. We can however help with technical logic and workflow design, so I’ll focus on that.
The Galaxy Workflow Library is a resource for HTP production workflows and can give some ideas about how processing steps are usually combined.
Classification steps
Please see the Microbiome category in the library above for taxonomic classification example workflows.
For upstream QC steps, visiting the Galaxy Training Network (GTN) might be helpful so I’ll link that too! FastQC is to assess quality but doesn’t involve trimming (if you read type needs that?). The usual path is FastQC → [some trimming tool] → FastQC → MultiQC. You may want to break that out into a distinct workflow, or move it into a sub-workflow.
Microbiome / Tutorial List- topic here with help and an example workflow template → Quality Control Start Here! multQC issue and guidance?
- then a very simple IWC workflow here → Short-read quality control and trimming | IWC
mapDamage
In addition to the tool form help, the original tool guide has some guidance about data content expectations. You could check your BAM to make sure your data fits these (example: FixMateInformation).
- mapDamage by the Orlando Group (
#Inputs)
Visualization/Reports
MultiQC supports all (most?) of the Samtools package, so you could put all of these together too.
Then, for customizing your report at the end, we have a tutorial that explains the basic functionality here.
I hope this helps and others are welcome to comment more!
Let’s also ping one of the developers who helped wrap this last tool for Galaxy to see if they have any suggestions! Hi @bernt-matthias would you like to comment?
I’ve also cross posted this topic over to the MicroGalaxy special interest group to see if anyone there has more to add! You can also join here!