Sample replicate processing

[A-Chalk]

Hello! I'm processing samples with multiple replicates, and I've found that the system works fine as long as the number of treated and untreated samples is the same. But in many cases, I have a single mock file and 2-8 treated samples.

I've tried setting my command script up with tsamp = "T1name, T2name, T3name..." and usamp = "U1name", but each time the pipeline gets stuck during overlap analysis:

"################ DELTA AND HITS ################ "
"CAST0CCR5OT0WTRNP0DUP_S1_L001 vs. CAST0CCR5OT0MOCK_S1"
"Error: File not found -> ../samples/CCR5_OT_WTRNP/U2/fastq_aln/CAST0CCR5OT0MOCK_S1_Alignment.bed"

"################ OVERLAP ANALYSIS ################"
"../samples/CCR5_OT_WTRNP/OVL2_SIGNIF1"
Error in read.xlsx.default(X[[i]], ...) : File does not exist.
Calls: runPipelineCRISPR ... getUnion -> lapply -> lapply -> FUN -> read.xlsx.default
Execution halted

I can get around this by simply duplicating the U1 file and changing the name slightly, but it massively increases the processing time because it treats each untreated file as a distinct sample. Is there a simpler way to do this?? Thank you!