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sunbeam-labs / sbx_report

Generates a final report, with figures, from a Sunbeam run
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Single-end Reads Cannot Generate Report #8

Open Lswhiteh opened 5 years ago

Lswhiteh commented 5 years ago

When running attempting to generate report on single end data, the error Quitting from lines 269-291 (.snakemake.u7zo7ih9.final_report.Rmd) Error in mutate_impl(.data, dots) : Evaluation error: object 'fwd_only' not found. Calls: <Anonymous> ... as.data.frame -> mutate -> mutate.tbl_df -> mutate_impl

halts execution. It seems to be expecting input from paired end reads based on where fwd_only is generated (the qc report of a sunbeam run), but when single end reads are analyzed it has no input.

Removing the decontamination section of the Rmd allows the job to run and report to be generated.

Output file with decontamination removed: https://gist.github.com/Lswhiteh/b752c02abfd2c7c3ec0902879c6b9d4b

eclarke commented 5 years ago

Good catch. We need to add a check to handle single-end reads here.

wangjiawen2013 commented 4 years ago

I met this error too, it seems that it has not been fixed now