refine_VIF_output.R fails when *.vif.evidence_counts.tsv is empty

[katgorski]

Description of the bug

So there weren't any interesting events in my sample and *vif.evidence_counts.tsv was empty, only had a header. Thus I wasn't able to generate the sample report defined in the SUMMARY_REPORT process because that file was empty--in refine_VIF_output.R, the resulting col types didn't match so it wasn't able to execute the join here:

viralintegration/bin/refine_VIF_output.R

Lines 53 to 55 in 70e558a

	vif_counts <- read.table(vif_counts_filename, header = T, sep = "\t", stringsAsFactors = F, comment.char = "", quote = "")
	data <- right_join(prelim_counts, vif_counts, by = "contig")

It should be a simple fix: define the column types when reading in the table initially, but because it's not originally your script/it's from the original pipeline you adapted, I'm not sure how much you want to modify it.

Command used and terminal output

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in `right_join()`:
  ! Can't join on `x$contig` x `y$contig` because of incompatible types.
  i `x$contig` is of type <character>>.
  i `y$contig` is of type <logical>>.
  Backtrace:
      x
   1. +-dplyr::right_join(prelim_counts, vif_counts, by = "contig")
   2. \-dplyr:::right_join.data.frame(prelim_counts, vif_counts, by = "contig")
   3.   \-dplyr:::join_mutate(...)
   4.     \-dplyr:::join_rows(...)
   5.       \-base::tryCatch(...)
   6.         \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   7.           \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.             \-value[[3L]](cond)
   9.               \-rlang::abort(bullets, call = error_call)
  Execution halted

Relevant files

No response

System information

• Nextflow version 23.10.1 build 5891
• Seqera platform to launch
• azurebatch
• nf-core/viralintegration v0.1.1 (70e558a)