Sarek possibly supplying the wrong number of args for CONTROLFREEC_ASSESSSIGNIFICANCE?

[SpikyClip]

Description of the bug

Ran into this controlfreec error trying to run sarek in paired mode:

Error in `$<-.data.frame`(`*tmp*`, Ratio, value = logical(0)) : 
  replacement has 0 rows, data has 828
Calls: $<- -> $<-.data.frame
Execution halted

I noticed that 4 files were supplied to the R script in this order:

cat $(which assess_significance.R) | R --slave --args PPMP022120320ANGIO_CELL_vs_PPMP022120320ANGIO_BCL.tumor.mpileup.gz_CNVs PPMP022120320ANGIO_CELL_vs_PPMP022120320ANGIO_BCL.tumor.mpileup.gz_normal_CNVs PPMP022120320ANGIO_CELL_vs_PPMP022120320ANGIO_BCL.tumor.mpileup.gz_normal_ratio.txt PPMP022120320ANGIO_CELL_vs_PPMP022120320ANGIO_BCL.tumor.mpileup.gz_ratio.txt

I am a bit confused by the contents of the R script, it seems to only take two tables as args and for some reason is calling from args[5] and args[4]:

args <- commandArgs()

dataTable <-read.table(args[5], header=TRUE);
ratio<-data.frame(dataTable)

dataTable <- read.table(args[4], header=FALSE)
cnvs<- data.frame(dataTable)

I suspect what is happening is that args[5] is returning NA causing issues. However, if that was the case I don't think this script would be working for anybody. I'm clearing missing something with how this script was written. Will try investigate it further by looking at runs that work, but I've already cleared out my cache for previously successful tumor-only runs.

Command used and terminal output

No response

Relevant files

controlfreec_assesssignificance_bug.zip

System information

System information

• Nextflow: 23.10.1, 23.04.5
• Hardware: HPC
• Executor: slurm
• Container engine: Singularity
• OS: Linux m3-login2 3.10.0-1160.71.1.el7.x86_64 #1 SMP Tue Jun 28 15:37:28 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
• nf-core/sarek: 3.4.0, 3.3.2