diff --git a/rules/build_illumina.smk b/rules/build_illumina.smk
index dd88c0a473fc06245eb7796d12b0d0971caae72e..c1bb0e9eddc56bb9bf37a8987423d6ed80363956 100644
--- a/rules/build_illumina.smk
+++ b/rules/build_illumina.smk
@@ -23,7 +23,7 @@ rule unzipFastq_R1:
 	input:
 		assembly=R1_gzipped,
 	output:
-		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/temp_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log"),
 	conda:
@@ -42,7 +42,7 @@ rule symlinkUnzippedFastq_R1:
 	input:
 		assembly=R1_notgzipped,
 	output:
-		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/temp_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
 	container:
 		None
 	shell:
@@ -54,7 +54,7 @@ rule unzipFastq_R2:
 	input:
 		assembly=R2_gzipped,
 	output:
-		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/temp_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
 	conda:
@@ -73,7 +73,7 @@ rule symlinkUnzippedFastq_R2:
 	input:
 		assembly=R2_notgzipped,
 	output:
-		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/temp_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
 	container:
 		None
 	shell:
@@ -84,9 +84,9 @@ rule symlinkUnzippedFastq_R2:
 
 rule trim10xbarcodes:
 	input:
-		read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
+		read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
 	output:
-		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq"),
+		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq"),
 	threads:
 		resource['trim10xbarcodes']['threads']
 	resources:
@@ -104,9 +104,9 @@ rule trim10xbarcodes:
 
 rule symlink_trim10xbarcodesR2:
 	input:
-		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/temp_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
 	output:
-		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq")
+		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq")
 	container:
 		None
 	shell:
@@ -118,11 +118,11 @@ rule symlink_trim10xbarcodesR2:
 
 rule symLink_trim10xbarcodes_notrimAdapt:
 	input:
-		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read1.fastq"),
-		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"),
+		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read1.fastq"),
+		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"),
 	output:
-		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_1.fq"),
-		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_2.fq")
+		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_1.fq"),
+		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_2.fq")
 	container:
 		None
 	shell:
@@ -133,11 +133,11 @@ rule symLink_trim10xbarcodes_notrimAdapt:
 
 rule symlinks_no10xOrAdaptTrim:
 	input:
-		read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R1.fastq"),
-		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq")
+		read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R1.fastq"),
+		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq")
 	output:
-		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_1.fq"),
-		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_2.fq")
+		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_1.fq"),
+		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_2.fq")
 	container:
 		None
 	shell:
@@ -148,11 +148,11 @@ rule symlinks_no10xOrAdaptTrim:
 
 rule symlinks_no10xwithAdaptTrim:
 	input:
-		read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R1.fastq"),
-		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq")
+		read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R1.fastq"),
+		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq")
 	output:
-		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read1.fastq"),
-		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read2.fastq")
+		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read1.fastq"),
+		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read2.fastq")
 	container:
 		None
 	shell:
@@ -163,14 +163,14 @@ rule symlinks_no10xwithAdaptTrim:
 
 rule trimAdapters:
 	input:
-		read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read1.fastq"),
-		read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"),
+		read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read1.fastq"),
+		read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"),
 	params:
-		outputDir=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/"),
+		outputDir=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/"),
 		r1_prefix="{readCounter}.{trim10x}.AdaptTrimmed",
 	output:
-		read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_1.fq")),
-		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_2.fq"))
+		read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_1.fq")),
+		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_2.fq"))
 	threads:
 		resource['trimAdapters']['threads']
 	resources:
@@ -187,13 +187,13 @@ rule trimAdapters:
 
 rule fastqc_Illumina:
 	input:
-		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"),
-		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
+		read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"),
+		read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
 	params:
-		folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc")
+		folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc")
 	output:
-		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"),
-		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html")
+		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"),
+		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html")
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_fastqc.log")
 	threads:
@@ -208,16 +208,16 @@ rule fastqc_Illumina:
 
 rule multiqc_hifi:
 	input:
-		read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
-		read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2])
+		read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
+		read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2])
 	params:
-		folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/"),
-		folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/05_multiqc/"),
-		filename="{sample}.{trim10x}.{trimAdapters}.multiqcReport.html"
+		folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/"),
+		folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/multiqc/"),
+		filename="{sample}.multiqcReport.html"
 	output:
-		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/05_multiqc/{sample}.{trim10x}.{trimAdapters}.multiqcReport.html")
+		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/multiqc/{sample}.multiqcReport.html")
 	log:
-		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.{trim10x}.{trimAdapters}_multiqc.log")
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.multiqc.log")
 	conda:
 		os.path.join(workflow.basedir, "envs/pigz.yaml")
 	shell:
@@ -227,7 +227,7 @@ rule multiqc_hifi:
 
 rule meryl_R1:
 	input:
-		read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq")
+		read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq")
 	params:
 		kmer = "{kmer}",
 	threads:
@@ -236,7 +236,7 @@ rule meryl_R1:
 		mem_mb=resource['meryl_R1']['mem_mb'],
 		time=resource['meryl_R1']['time'],
 	output:
-		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl"))
+		temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl")))
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R1.{kmer}.log")
 	priority:
@@ -251,7 +251,7 @@ rule meryl_R1:
 
 rule meryl_R2:
 	input:
-		read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
+		read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
 	params:
 		kmer = "{kmer}",
 	threads:
@@ -260,7 +260,7 @@ rule meryl_R2:
 		mem_mb=resource['meryl_R2']['mem_mb'],
 		time=resource['meryl_R2']['time'],
 	output:
-		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl"))
+		temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl")))
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R2.{kmer}.log")
 	priority:
@@ -276,24 +276,24 @@ rule meryl_R2:
 
 rule meryl_illumina_build:
 	input:
-		removeReads1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
-		removeReads2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
-		read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[wildcards.sample][2]),
-		read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[wildcards.sample][2])
+		# removeReads1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
+		# removeReads2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
+		read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[wildcards.sample][2]),
+		read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[wildcards.sample][2])
 	params:
-		removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/"),
-		removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/"),
+		removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/"),
+		removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/"),
 		kmer = "{kmer}",
-		path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/")
+		path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/")
 	threads:
 		resource['meryl_illumina_build']['threads']
 	resources:
 		mem_mb=resource['meryl_illumina_build']['mem_mb'],
 		time=resource['meryl_illumina_build']['time'],
 	output:
-		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/complete_{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl")),
+		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/complete_illumina.{sample}.{kmer}.meryl")),
 	log:
-		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}_hifi_{kmer}.{trim10x}.{trimAdapters}.log")
+		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.illumina_meryl.{kmer}.log")
 	priority:
 		10
 	conda: