Merged tables not produced if not run with --run_profile_standardisation

nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

https://nf-co.re/taxprofiler

MIT License

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Merged tables not produced if not run with --run_profile_standardisation #494

Open apalleja opened 3 months ago

apalleja commented 3 months ago

Description of feature

I was running taxprofiler mapping reads to metaphlan and I was not obtaining a combined report table until I used --run_profilestandardisation (following @jfy133 advice). I think it is not obvious the link between this parameter and obtaining the combined report table (metaphlan_combined_reports.txt). Perhaps it needs to be explained in the parameters explanations/help text or an additional flag should be created for that?

jfy133 commented 3 months ago

Thanks @apalleja !

my feeling we should have a separate subworkflow with it's own distinct parameter indeed. The behaviour of e.g. krakentools or metaphlan mergetables is not really standardisation.