diff --git a/Snakefile b/Snakefile
index 7ed7d9f05d55526518594587f8d339ee91c583c2..397ee4cbc662e61897642c803e7c38c5e5f92d59 100644
--- a/Snakefile
+++ b/Snakefile
@@ -36,7 +36,7 @@ def to_be_smrtTrimmed(userAnswer):
 
 samples = pd.read_csv(config['samplesTSV'], dtype=str, index_col=False, delim_whitespace=True, skip_blank_lines=True)
 if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'trimAdapters', 'fastQC']).issubset(samples.columns):
-	whichRule = "rules/illumina.smk"
+	whichRule = "rules/illumina_05_11_21.smk"
 	samples=samples.reset_index()
 	samples['readCounter'] = samples.groupby(['sample']).cumcount()+1
 	samples['readCounter'] = samples['readCounter'].astype(str)
@@ -103,7 +103,7 @@ if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'tri
 	ruleAll=[expand(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl"), sample=key, kmer=value1, trim10x=value2, trimAdapters=value3) for key, [value1, value2, value3] in testDict.items()]
 
 elif set(['sample', 'hifi_reads', 'meryl_kmer_size'	,'trimSMRTbell', 'fastQC']).issubset(samples.columns):
-	whichRule = "rules/hifi.smk"
+	whichRule = "rules/hifi_05_11_21.smk"
 	samples=samples.reset_index()
 	samples['readCounter'] = samples.groupby(['sample']).cumcount()+1
 	samples['readCounter'] = samples['readCounter'].astype(str)
@@ -171,10 +171,10 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size'	,'trimSMRTbell', 'fastQC']).
 	ruleAllQCFiles=[]
 
 	if samples['fastQC'].str.contains('True').any():
-		ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{sample}.multiqcReport.html"), sample=key, smrtornot=value1) for key, [value1, value2] in testDictQC.items()]
-	ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/03_merylDb/complete_hifi_{sample}_dB.{kmer}.meryl"), sample=key, kmer=value1, smrtornot=value2) for key, [value1, value2] in testDict.items()]
+		ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html"), sample=key, smrtornot=value1) for key, [value1, value2] in testDictQC.items()]
+	ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl"), sample=key, kmer=value1, smrtornot=value2) for key, [value1, value2] in testDict.items()]
 elif set(['ID',	'PRI_asm', 'ALT_asm',	'merylDB',	'merylDB_kmer', 'genomeSize']).issubset(samples.columns):
-	whichRule = "rules/run.smk"
+	whichRule = "rules/run_05_11_21.smk"
 	samples['genomeSize'] = samples['genomeSize'].fillna(0)
 	samples["genomeSize"] = pd.to_numeric(samples["genomeSize"])
 
diff --git a/installGEP.yaml b/installGEP.yaml
index 4f1f395ed78224b335e351e419531fb6ffb9f2b1..55edd6f1d557f89b018c09ebf69bdf2ca328f2e8 100644
--- a/installGEP.yaml
+++ b/installGEP.yaml
@@ -9,3 +9,4 @@ dependencies:
  - tabulate=0.8.7
  - beautifulsoup4=4.9
  - mamba=0.15.2
+ - pandoc=2.16.1
diff --git a/rules/hifi_05_11_21.smk b/rules/hifi_05_11_21.smk
index 83bd0aee4e3673384b178f35d3d6d00224a2bb76..2648a562c8590bc90ae552c5a2ef17a1bb2d3670 100644
--- a/rules/hifi_05_11_21.smk
+++ b/rules/hifi_05_11_21.smk
@@ -33,7 +33,7 @@ rule unzipHifi:
 	input:
 		fastq=hifi_gzipped,
 	output:
-		temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")),
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
 	conda:
@@ -47,7 +47,7 @@ rule symlinkUnzippedHifi:
 	input:
 		fastq=hifi_notgzipped,
 	output:
-		temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")),
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
 	shell:
@@ -98,7 +98,7 @@ rule symlinkfornotSmartTrimmed:
 	input:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
 	output:
-		outputFile=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.notsmrtTrimmed.fastq"))
+		outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.notsmrtTrimmed.fastq")
 	shell:
 		"""
 		ln -s {input} {output.outputFile}
@@ -110,25 +110,28 @@ rule fastqc_hifi_SMRT_removed:
 	params:
 		folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/")
 	output:
-		os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html")
+		os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html")
 	threads: 1
 	log:
-		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{readCounter}.{smrtornot}.FastQC.log")
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}.{smrtornot}.FastQC.log")
 	conda:
 		"../envs/pigz.yaml"
 	shell:
-		"(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}"
+		"""
+		mkdir {params.folder2out}
+		(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}
+		"""
 
 rule multiqc_hifi_SMRTremoved:
 	input:
-		lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], smrtornot=testDict[wildcards.sample][1])
+		lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], smrtornot=testDict[wildcards.sample][1])
 	params:
-		folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/"),
+		folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/"),
 		filename="{sample}.{smrtornot}.multiqcReport.html"
 	output:
-		os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html")
+		os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html")
 	log:
-		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{sample}.{smrtornot}.multiqc.log")
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.{smrtornot}.multiqc.log")
 	conda:
 		"../envs/pigz.yaml"
 	shell:
@@ -146,18 +149,17 @@ rule meryl_hifi_trimmed_count:
 		kmer = "{kmer}"
 #		path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
 	threads:
-		workflow.cores
+		workflow.cores * 0.25
 	output:
-		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/03_merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl")),
+		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl")),
 	log:
-		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log")
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log")
 	priority:
 		10
 	conda:
 		"../envs/merylMerq_2.yaml"
 	shell:
 		"""
-		export OMP_NUM_THREADS={threads}
 		(meryl count k={params.kmer} threads={threads} {input.reads} output {output}) &> {log}
 		"""
 
@@ -165,24 +167,23 @@ rule meryl_hifi_build:
 	input:
 #		reads= rules.trimSMRTbell.output.outputFile
 #		lambda wildcards: expand(config['Results'],"{group}/alignment/{sample}.bam", group=wildcards.group, sample=GROUPS[wildcards.group]
-		lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/03_merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl"), sample=wildcards.sample, readCounter=d[wildcards.sample], kmer=testDict[wildcards.sample][0], smrtornot=testDict[wildcards.sample][1])
+		lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl/"), sample=wildcards.sample, readCounter=d[wildcards.sample], kmer=testDict[wildcards.sample][0], smrtornot=testDict[wildcards.sample][1])
 #		reads=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{readCounter}" + "_hifi_dB.21.meryl")
 	params:
 		kmer = "{kmer}"
 	threads:
-		workflow.cores
+		workflow.cores * 0.5
 	output:
-		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}")),
+		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl")),
 	log:
-		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{sample}_hifi_{smrtornot}.{kmer}.log")
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}_hifi_{smrtornot}.{kmer}.log")
 	priority:
 		10
 	conda:
 		"../envs/merylMerq_2.yaml"
 	shell:
 		"""
-		export OMP_NUM_THREADS={threads}
-		(meryl union-sum k={params.kmer} threads={threads} {input} output {output}) &> {log}
+		(meryl union-sum {input} output {output}) &> {log}
 		"""
 #
 #
diff --git a/rules/illumina_05_11_21.smk b/rules/illumina_05_11_21.smk
index de12cc7bcb186884e1df91d49204678d5b274c21..b8729f913e9f11f4a6eedef4766532d832495813 100644
--- a/rules/illumina_05_11_21.smk
+++ b/rules/illumina_05_11_21.smk
@@ -40,7 +40,7 @@ rule unzipFasta_R1:
 	input:
 		assembly=R1_gzipped,
 	output:
-		temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq")),
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log")
 	conda:
@@ -64,7 +64,7 @@ rule unzipFasta_R2:
 	input:
 		assembly=R2_gzipped,
 	output:
-		temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq")),
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
 	conda:
@@ -88,10 +88,10 @@ rule symlinkUnzippedFasta_R2:
 rule trim10xbarcodes:
 	input:
 		read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
-		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
+#		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
 	output:
 		read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq")),
-		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq"))
+#		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq"))
 	threads:
 		workflow.cores * 0.125
 	log:
@@ -101,12 +101,23 @@ rule trim10xbarcodes:
 	shell:
 		"""
 		(trimmomatic SE -threads {threads} {input.read1} {output.read1} HEADCROP:23) &> {log}
-		ln -s {input.read2} {output.read2}
 		"""
+#		ln -s {input.read2} {output.read2}
 
 
-
-
+rule trim10xbarcodesR2:
+	input:
+		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
+	output:
+		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq"))
+	threads:
+		1
+	conda:
+		"../envs/pigz.yaml"
+	shell:
+		"""
+		ln -s {input.read2} {output.read2}
+		"""
 
 
 
@@ -274,6 +285,5 @@ rule meryl_hifi_build:
 		"../envs/merylMerq_2.yaml"
 	shell:
 		"""
-		export OMP_NUM_THREADS={threads}
-		(meryl union-sum k={params.kmer} threads={threads} {input} output {output}) &> {log}
+		(meryl union-sum {input} output {output}) &> {log}
 		"""
diff --git a/rules/run_05_11_21.smk b/rules/run_05_11_21.smk
index c2c847181aa2124dbd736cf5d7db10a7aaef5c47..e4bcc42d98ba5edecde6aef89e0fa8083b70de22 100644
--- a/rules/run_05_11_21.smk
+++ b/rules/run_05_11_21.smk
@@ -87,7 +87,7 @@ rule busco5:
 		assemblyName = "{asmID}",
 		chngDir = os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO")
 	threads:
-		workflow.cores * 0.5
+		workflow.cores * 0.125
 	output:
 #		report(os.path.join(config['Results'], "{sample}" + "/busco5/" + "{sample}" + "/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt"), caption="../report/busco.rst", category="Benchmark Universal Single Copy Orthologs", subcategory="{fastq}")
 		os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO/{asmID}/short_summary.specific." + buscoDataBaseName + "_odb10.{asmID}.txt"),
@@ -149,7 +149,7 @@ rule merqury:
 		# symlink_fasta=os.path.join(config['Results'], "01_evaluation/{asmID}/01B_QV-and-kmerMultiplicity/{asmID}.fasta"),
 		symlink_merylDB=directory(os.path.join(config['Results'], "1_evaluation/{asmID}/04_merquryQVandKAT/merylDB_providedFor_{asmID}.meryl"))
 	threads:
-		workflow.cores * 0.5
+		workflow.cores * 0.125
 	output:
 		os.path.join(config['Results'],"1_evaluation/{asmID}/04_merquryQVandKAT/{asmID}_merqOutput.qv"),
 		os.path.join(config['Results'],"1_evaluation/{asmID}/04_merquryQVandKAT/{asmID}_merqOutput.completeness.stats"),
@@ -529,7 +529,7 @@ rule makeReport:
 		os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.completeness.stats"),
 		os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/only_buscoScores_{asmID}.txt"),
 		os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.{asmID}.PRI.spectra-cn.fl.png"),
-		os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.spectra-cn.fl.png")
+		os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.{asmID}.PRI.spectra-cn.st.png")
 	params:
 		"{asmID}",
 		"{kmer}",