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BeeCSI-Microbiome / taxonomic_profiling_pipeline

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Krona visualization #3

Closed ropolomx closed 2 years ago

ropolomx commented 2 years ago

Goal: to generate Krona interactive visualizations of multiple samples in one, like in this example.

LLansing commented 2 years ago

We could make a rule in the Snakemake workflow to perform Krona on the Kraken output table. In the future, if we're using the mag pipeline, Krona is integrated.

ropolomx commented 2 years ago

Thanks @LLansing. Your options are:

  1. Add this to Snakemake; or
  2. If it is in the nf-core/mag wofklow, and we are happy with its functioning in Biocluster then use that... but I don't think it combines multiple samples in one visualization. It generates one visualization per sample.

So something would need to get modified either in Snakemake or Nextflow.