Reporting Kraken output in Sunbeam
0
0
Entering edit mode
3.4 years 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 • 715 views
ADD COMMENT

Login before adding your answer.

Traffic: 2004 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6