Single-end Reads Cannot Generate Report

[Lswhiteh]

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]

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

[wangjiawen2013]

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