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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Show available Guppy and Medaka models #142

Closed hoelzer closed 2 years ago

hoelzer commented 3 years ago

This came up while other ("non-nanopore-experienced") users were running poreCov. Besides the default models for guppy and medaka would it be possible to add information on the available models? Either via something like 

nextflow run replikation/poreCov --show_guppy_models --show_medaka_models

or in the README.md? The defaults are now w/ 0.10.0 the sup models for both but what if people get already fastq data as input. Or want to compare different models but are not sure what the exact high or fast model names are. In such a case, this would be helpful.

Maybe (and if this is available) linking out to some other resources that have this information on guppy/medaka models would be already enough.

hoelzer commented 3 years ago

Ah and in this context it would be helpful to have both models also in the HTML report.

RaverJay commented 2 years ago

(I'm back from holidays)

What was used is asily available - will add to the report: params.guppy_model params.medaka_model

What models are available in general is dependent on what is in the guppy / ARTIC container and might change behind the scenes - I don't see an easy way to get this info? Maybe make processes that run the containers, only to run guppy_basecaller --list_workflows ? seems clunky

hoelzer commented 2 years ago

(wb!)

What was used is asily available - will add to the report: params.guppy_model params.medaka_model

Great, thx.

What models are available in general is dependent on what is in the guppy / ARTIC container and might change behind the scenes - I don't see an easy way to get this info? Maybe make processes that run the containers, only to run guppy_basecaller --list_workflows ? seems clunky

Yeah, agree. Could be just something to add to the "Troubleshooting" paragraph in the README? For us such stuff is basically clear, but for others just jumping w/ poreCov into ONT analyses they often feel lost w/ the correct models/params w/o even knowing what's available. So we could just add something like: click here to check available models or run xyz to get info.