Reporting Kraken output in Sunbeam
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11 months ago

I am trying to create a report from my Sunbeam results. I am using the latest dev version of Sunbeam, with sunbeam and this extension for creating the report. https://github.com/sunbeam-labs/sbx_report Although I am following the instructions on the git hub repository, I run into an error with the final_report.Rmd file.

"summarise() regrouping output by 'Direction' (override with .groups argument) Quitting from lines 281-303 (tmppkoc7wxa.final_report.Rmd) Error: Problem with mutate() input low_quality. object 'fwd_only' not found Input low_quality is (fwd_only + rev_only + dropped)/input"

I've opened an issue for the problem in the repository, where the whole error message can be found: https://github.com/sunbeam-labs/sbx_report/issues/15 I am wondering, what could be the problem, what am I doing wrong and are there other tools for creating a similar report?

Thanks in advance!

metagenome sunbeam conda kraken2 multiqc • 260 views
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