diff --git a/.DS_Store b/.DS_Store
index 5b72387d5cbba55edf7bad03f3912bd1c763ac59..b772272316d68012d461a11782678cd6932c77f3 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/programs/.DS_Store b/programs/.DS_Store
index 54b7e113f4461e5b893542b74cd8285135498795..62cf363b4ffd08bcddfc2d41efafcdf2186d7794 100644
Binary files a/programs/.DS_Store and b/programs/.DS_Store differ
diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk
index 348580085c7954df31fe21d9ae835c9bbbf5a0d7..230f47d5658fd54fa1f32fffcbe13be7dd747a03 100644
--- a/rules/rulesNew.smk
+++ b/rules/rulesNew.smk
@@ -239,8 +239,8 @@ rule merqury:
 		workflow.cores * 0.5
 	output:
 		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"), caption="../report/merqury/qvScore.rst", category="QV Estimate", subcategory="{sample}"),
-		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png"), caption="../report/merqury/spectra-cn_stacked.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
-		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
+		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"), caption="../report/merqury/spectra-cn_stacked.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
+		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
 		os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist")
 	log:
 		os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log")
@@ -268,8 +268,8 @@ rule merqury:
 rule genomescope2:
 	input:
 		hist=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
-		check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"),
-		check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png")
+		check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
+		check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png")
 	params:
 		outFolder=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/"),
 		cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_dB.21.histo")
@@ -347,8 +347,8 @@ rule saveConfiguration_and_getKeyValues:
 		gscopeLin=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"),
 		busco=os.path.join(config['Results'], "{sample}" + "/1_busco5/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
 		qv=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"),
-		spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.st.png"),
-		spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.spectra-cn.fl.png"),
+		spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
+		spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
 #		os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
 #		os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
 		scaffStats=os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_scaffold_stats.tsv"),
@@ -372,8 +372,8 @@ rule saveConfiguration_and_getKeyValues:
 		gscopeLin=os.path.join(config['Results'], "{sample}" +"/5_Key_Results/" + "{sample}" + "_gScope_linear_plot.png"),
 		busco=os.path.join(config['Results'], "{sample}" + "/5_Key_Results/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
 		qv=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.qv"),
-		spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.spectra-cn.st.png"),
-		spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.spectra-cn.fl.png"),
+		spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
+		spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
 #		os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
 #		os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
 		scaffStats=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/{sample}_scaffold_stats.tsv"),