Attempt fixing heatmap script, but does not yet work

Snakefile

@@ -48,7 +48,7 @@ rule simul:
                 sample = ["simulation7","simulation8","simulation9"],
                 window = [50000, 100000]),
         expand("evaluation/simulation{seed}_{window}.{segments}.pdf",
-                seed  = [7,8,9],
+                seed  = list(range(5)),
                 window = [50000, 100000],
                 segments = ["few","medium","many"])
 
@@ -376,14 +376,14 @@ rule run_sv_classification:
                 utils/R-packages2/ > {log} 2>&1
         """
 
-rule convert_SVprob_output:
+rule plot_heatmap:
     input:
         haplotypeProbs = "sv_probabilities/{sample}/{windows}.{bpdens}/allSegCellProbs.table",
         genotypeProbs  = "sv_probabilities/{sample}/{windows}.{bpdens}/allSegCellGTprobs.table",
         info     = "counts/{sample}/{windows}.info",
         bamNames = "sv_probabilities/{sample}/{windows}.{bpdens}/bamNames.txt"
     output:
-        "sv_probabilities/{sample}/{windows}.{bpdens}/final_plots/"
+        "sv_probabilities/{sample}/{windows}.{bpdens}/final_plots/heatmapPlots.pdf"
     log:
         "log/{sample}/final.plots.{windows}.{bpdens}.txt"
     script:

utils/plot_heatmap.R

@@ -163,13 +163,12 @@ plotHeatmapSegment <- function(dataFrame, plot.log=FALSE, file=NULL, aggProbs=F,
 
 
 GTprobsFile = snakemake@input[["genotypeProbs"]]
-directory = snakemake@input[[1]]
 
 GTprobs <- read.table(GTprobsFile, stringsAsFactors = F, header = T )
 ID <- apply(GTprobs[,c('chr','start','end')], 1, function(x) paste(x, collapse = "_"))
 
 GTprobs.l <- split(GTprobs, paste(GTprobs$chr, GTprobs$start, GTprobs$end))
 
-pdf(paste0(directory, "heatmapPlots.pdf"))
+pdf(snakemake@output[[1]])
 lapply(GTprobs.l, plot)
 dev.off()