diff --git a/bin/plot_markers1.R b/bin/plot_markers1.R
index 159ae4f..3cf0faa 100755
--- a/bin/plot_markers1.R
+++ b/bin/plot_markers1.R
@@ -19,7 +19,11 @@ colnames(karyotype1) <- c("Chr", "End", "Start", "species", "size", "color")
 # reorder columns
 karyotype <- karyotype1[, c(1,3,2,4,5,6)]
 
-write.table(karyotype, file = paste0("data/karyotype/", out_name, "_karyotype.txt"), quote = FALSE, row.names = FALSE, col.names = TRUE, sep = "\t")
+# debugging code
+print("Karyotype table\n")
+head(karyotype)
+
+write.table(karyotype, file = paste0(out_name, "_karyotype.txt"), quote = FALSE, row.names = FALSE, col.names = TRUE, sep = "\t")
 
 
 
diff --git a/bin/plot_markers2.R b/bin/plot_markers2.R
deleted file mode 100755
index 28c52dd..0000000
--- a/bin/plot_markers2.R
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env Rscript
-
-# load libraries
-require(RIdeogram)
-
-# From the Rstudio console set working directory "plot_markers/" folder:
-# setwd("/path/to/support_protocol2/plot_markers/")
-
-
-karyotype_file <- "./data/karyotype/Dmel_karyotype.txt"  # provide path to karyotype file 
-coordinates <- "./plot_results/Dmel_busco_coordinates.txt" # provide path to markers' coordinates
-out_name <- "Dmel" # sample name
-
-# load karyotype
-karyotype <- read.csv(karyotype_file, sep="\t", header = TRUE, stringsAsFactors = F)
-
-# load mapping busco_coordinates.txt
-busco_mappings <- read.csv(coordinates, sep="\t", header = FALSE, stringsAsFactors = F)
-
-colnames(busco_mappings)[1] <- "Status"
-colnames(busco_mappings)[2] <- "Chr"
-colnames(busco_mappings)[3] <- "Start"
-colnames(busco_mappings)[4] <- "End"
-
-busco_mappings$Type <- "BUSCO_marker"
-busco_mappings$Shape <- "circle" 
-
-# change status in color
-busco_mappings$Status <- gsub("Complete", '2dacd6', busco_mappings$Status)
-busco_mappings$Status <- gsub("Duplicated", '0a0e1a', busco_mappings$Status)
-busco_mappings$Status <- gsub("Fragmented", 'eded13', busco_mappings$Status)
-colnames(busco_mappings)[1] <- "color"
-
-busco_mappings <- busco_mappings[, c(5,6,2,3,4,1)]
-
-ideogram(karyotype = karyotype, label = busco_mappings, label_type = "marker", output = paste0(out_name, ".svg"))
-# convert to png
-convertSVG(paste0(out_name, ".svg"), device = "png")
-
diff --git a/conf/modules.config b/conf/modules.config
index a768dc5..3781d81 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -159,6 +159,14 @@ process {
         ]
     }
 
+    withName: 'GENOME_BUSCO_IDEOGRAM' {
+        publishDir = [
+            path: { "${params.outdir}/genome_busco_ideogram" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'GENE_OVERLAPS' {
         publishDir = [
             path: { "${params.outdir}/gene_overlaps" },
diff --git a/modules/local/genome_ideogram.nf b/modules/local/genome_ideogram.nf
index ad73ff5..5a3dde8 100644
--- a/modules/local/genome_ideogram.nf
+++ b/modules/local/genome_ideogram.nf
@@ -19,15 +19,22 @@ process GENOME_BUSCO_IDEOGRAM {
     """
     grep -v "#" ${busco_full_table} | cut -f 2,3,4,5  | grep -v "Missing" > ${prefix}_busco_coordinates.txt
 
+    #echo "Current directory: \$(pwd)"
+    #echo "Contents of current directory:"
+    #ls -l
+    #echo "Contents of projectDir:"
+    #ls -l $projectDir/bin
+    #echo "Contents of plot_markers1.R script"
+    #cat $projectDir/bin/plot_markers1.R
 
     # Get chromosome lengths:
     seqkit fx2tab -i -n -l ${genome} > ${prefix}_for_karyotype.txt
     
     # Call script for table wrangling
-    Rscript /home/ucbtfrd/pipelines/genomeqc/bin/plot_markers1.R ${prefix}_for_karyotype.txt ${prefix}
+    $projectDir/bin/plot_markers1.R ${prefix}_for_karyotype.txt ${prefix}
 
     # Call script for plotting
-    Rscript /home/ucbtfrd/pipelines/genomeqc/bin/plot_markers2.R ${prefix}_karyotype.txt ${prefix}_busco_coordinates.txt ${prefix}
+    $projectDir/bin/plot_busco_ideogram.R --busco_output ${prefix}_busco_coordinates.txt --karyotype ${prefix}_karyotype.txt --prefix ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf
index f7c1a66..658aa39 100644
--- a/modules/nf-core/busco/busco/main.nf
+++ b/modules/nf-core/busco/busco/main.nf
@@ -4,8 +4,8 @@ process BUSCO_BUSCO {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0':
-        'biocontainers/busco:5.7.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.8.0--pyhdfd78af_0':
+        'biocontainers/busco:5.8.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta, stageAs:'tmp_input/*')