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cvdelannoy / poreTally

Benchmark MinION assembler pipelines and publish your results in a heartbeat!
MIT License
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multiqc template assembler_benchmark #7

Open chienchi opened 5 years ago

chienchi commented 5 years ago

Hi,

Thanks for the great tool on nanopore data assembly benchmark. I ran a dataset and it failed on mulitqc step which compliant about the tempate invalid. 

Error: Invalid value for "-t" / "--template": invalid choice: assembler_benchmark. (choose from default, default_dev, geo, simple, sections)

Does poreTelly developed a template for multiqc?

Thanks, Chienchi

cvdelannoy commented 5 years ago

Hi Chienchi,

Thank you, and sorry for the late reply! Yes, poreTally relies on a custom template, but it should download an adapted version of multiqc containing that template automatically during the run.

The only scenario in which I guess this could happen is if you have a pre-existing installlation of multiqc and somehow that one is accidentally activated, but I couldn't reproduce such a scenario, with any number of additional pip/conda installed multiqc versions

Do you have another multiqc installation on your machine that could perhaps cause this issue? Does the problem persist if you install poreTally in a new conda environment?