diff --git a/Snakefile b/Snakefile
index b950ae0b78c6f864e92d0644c2542a4086aff8a9..5c775d64921f519a2a12850c6a2121a93768c39f 100644
--- a/Snakefile
+++ b/Snakefile
@@ -53,7 +53,7 @@ def which_analysis():
         )
     if config["run_Quast"] == "True": # Running quast on haplotypes
         analysis_inputs.append(
-            expand("output/quast/{haplotype}.quast.html", haplotype=SAMPLES_NOREF)
+            "output/quast/Quast.report.html"
         )
     if config["get_contig_pos"] == "True": # Contig position in chromosomes figure
         analysis_inputs.append(
@@ -130,11 +130,11 @@ rule ragtag_scaffolding:
 rule quast_stats:
     # Run Quast on ragtagged genomes
     input:
-        fa="data/haplotypes/{haplotype}.fa.gz",
+        fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
         ref="data/haplotypes/"+config['reference']
     output:
-        report="output/quast/{haplotype}.quast.html"
-    threads: 8
+        report="output/quast/Quast.report.html"
+    threads: workflow.cores//2
     params:
         apppath=config["app.path"],
         panname=config["name"]
@@ -142,22 +142,22 @@ rule quast_stats:
         """
         apptainer run {params.apppath}/pan1c-env.sif quast.py \
             -t {threads} \
-            -o "$(dirname {output.report})/{wildcards.haplotype}" \
+            -o "$(dirname {output.report})" \
             -r {input.ref} \
             --plots-format png \
             --no-read-stats \
+            --no-icarus \
             -s \
             --large \
-            {input.fa}
+            {input.fas}
 
         # Compressing temporary files
         apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
-            -@ {threads} $(dirname {output.report})/{wildcards.haplotype}/contigs_reports/*.fa
+            -@ {threads} $(dirname {output.report})/contigs_reports/*.fa
         apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
-            -@ {threads} $(dirname {output.report})/{wildcards.haplotype}/contigs_reports/minimap_output/*
+            -@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
 
-        mv $(dirname {output.report})/{wildcards.haplotype}/report.html $(dirname {output.report})/{wildcards.haplotype}/$(basename {output.report})
-        ln -s $(pwd)/$(dirname {output.report})/{wildcards.haplotype}/$(basename {output.report}) {output.report}
+        mv $(dirname {output.report})/report.html {output.report}
         """
 
 rule contig_position:
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index be14a263ee9b92fef6b09d789bd3edf198fd9a00..7ccd486af6227e20d36950d4ae344f150748a636 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -35,12 +35,12 @@ my.cytobands <- toGRanges(x)
 pp <- getDefaultPlotParams(plot.type=1)
 pp$ideogramheight <- 200
 pp$data1outmargin <- 50
-pp$leftmargin <- 0.25
+pp$leftmargin <- 0.28
 pp$rightmargin <- 0
 pp$data1height <- 0
 pp$data2height <- 0
 
-png(opt$out, width=2000, height=2000, pointsize=6, res=300, antialias = "none")
+png(opt$out, width=2780, height=500, pointsize=6, res=300, antialias = "none")
 kp <- plotKaryotype(genome=my.genome, cytobands=my.cytobands, plot.params=pp, chromosomes="all")
 kp <- kpAddBaseNumbers(kp, cex=0.6, tick.dist=5000000)
 dev.off()
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