diff --git a/workflow/Snakefile b/workflow/Snakefile
index 7bc435a..c1c8f8f 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -210,26 +210,26 @@ rule cutadapt:
 if [ ! -d {params.outdir} ];then mkdir {params.outdir};fi
 if [ "{params.peorse}" == "PE" ];then
 	## Paired-end
-	cutadapt --pair-filter=any \
-	--nextseq-trim=2 \
-	--trim-n \
-	-n 5 -O 5 \
-	-q 10,10 -m {params.cutadapt_min_length}:{params.cutadapt_min_length} \
-	-b file:{params.adapters} \
-	-B file:{params.adapters} \
-	-j {threads} \
-	-o {output.of1} -p {output.of2} \
+	cutadapt --pair-filter=any \\
+	--nextseq-trim=2 \\
+	--trim-n \\
+	-n 5 -O 5 \\
+	-q 10,10 -m {params.cutadapt_min_length}:{params.cutadapt_min_length} \\
+	-b file:{params.adapters} \\
+	-B file:{params.adapters} \\
+	-j {threads} \\
+	-o {output.of1} -p {output.of2} \\
 	{input.R1} {input.R2}
 else
 	## Single-end
-	cutadapt \
-	--nextseq-trim=2 \
-	--trim-n \
-	-n 5 -O 5 \
-	-q 10,10 -m {params.cutadapt_min_length} \
-	-b file:{params.adapters} \
-	-j {threads} \
-	-o {output.of1} \
+	cutadapt \\
+	--nextseq-trim=2 \\
+	--trim-n \\
+	-n 5 -O 5 \\
+	-q 10,10 -m {params.cutadapt_min_length} \\
+	-b file:{params.adapters} \\
+	-j {threads} \\
+	-o {output.of1} \\
 	{input.R1}
 	touch {output.of2}
 fi
@@ -284,29 +284,29 @@ if [ "{params.peorse}" == "PE" ];then
 	overhang=$(zcat {input} | awk -v maxlen=100 'NR%4==2 {{if (length($1) > maxlen+0) maxlen=length($1)}}; END {{print maxlen-1}}')
 	echo "sjdbOverhang for STAR: ${{overhang}}"
 	cd {params.outdir}
-	STAR --genomeDir {params.starindexdir} \
-	--outSAMstrandField None  \
-	--outFilterMultimapNmax 20 \
-	--alignSJoverhangMin 8 \
-	--alignSJDBoverhangMin 1 \
-	--outFilterMismatchNmax 999 \
-	--outFilterMismatchNoverLmax 0.3  \
-	--alignIntronMin 20 \
-	--alignIntronMax 1000000 \
-	--alignMatesGapMax 1000000 \
-	--readFilesIn {input.R1} {input.R2} \
-	--readFilesCommand zcat \
-	--runThreadN {threads} \
-	--outFileNamePrefix {params.sample}_p1. \
-	--chimSegmentMin 20 \
-	--chimMultimapNmax 10 \
-	--chimOutType Junctions \
-	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \
-	--outSAMtype None \
-	--alignEndsProtrude 10 ConcordantPair \
-	--outFilterIntronMotifs None \
-	--sjdbGTFfile {params.gtf} \
-	--outTmpDir=${{TMPDIR}} \
+	STAR --genomeDir {params.starindexdir} \\
+	--outSAMstrandField None  \\
+	--outFilterMultimapNmax 20 \\
+	--alignSJoverhangMin 8 \\
+	--alignSJDBoverhangMin 1 \\
+	--outFilterMismatchNmax 999 \\
+	--outFilterMismatchNoverLmax 0.3  \\
+	--alignIntronMin 20 \\
+	--alignIntronMax 1000000 \\
+	--alignMatesGapMax 1000000 \\
+	--readFilesIn {input.R1} {input.R2} \\
+	--readFilesCommand zcat \\
+	--runThreadN {threads} \\
+	--outFileNamePrefix {params.sample}_p1. \\
+	--chimSegmentMin 20 \\
+	--chimMultimapNmax 10 \\
+	--chimOutType Junctions \\
+	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \\
+	--outSAMtype None \\
+	--alignEndsProtrude 10 ConcordantPair \\
+	--outFilterIntronMotifs None \\
+	--sjdbGTFfile {params.gtf} \\
+	--outTmpDir=${{TMPDIR}} \\
 	--sjdbOverhang $overhang
 
 else
@@ -315,29 +315,29 @@ else
 	overhang=$(zcat {input.R1} | awk -v maxlen=100 'NR%4==2 {{if (length($1) > maxlen+0) maxlen=length($1)}}; END {{print maxlen-1}}')
 	echo "sjdbOverhang for STAR: ${{overhang}}"
 	cd {params.outdir}
-	STAR --genomeDir {params.starindexdir} \
-	--outSAMstrandField None  \
-	--outFilterMultimapNmax 20 \
-	--alignSJoverhangMin 8 \
-	--alignSJDBoverhangMin 1 \
-	--outFilterMismatchNmax 999 \
-	--outFilterMismatchNoverLmax 0.3  \
-	--alignIntronMin 20 \
-	--alignIntronMax 1000000 \
-	--alignMatesGapMax 1000000 \
-	--readFilesIn {input.R1} \
-	--readFilesCommand zcat \
-	--runThreadN {threads} \
-	--outFileNamePrefix {params.sample}_p1. \
-	--chimSegmentMin 20 \
-	--chimMultimapNmax 10 \
-	--chimOutType Junctions \
-	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \
-	--outSAMtype None \
-	--alignEndsProtrude 10 ConcordantPair \
-	--outFilterIntronMotifs None \
-	--sjdbGTFfile {params.gtf} \
-	--outTmpDir=${{TMPDIR}} \
+	STAR --genomeDir {params.starindexdir} \\
+	--outSAMstrandField None  \\
+	--outFilterMultimapNmax 20 \\
+	--alignSJoverhangMin 8 \\
+	--alignSJDBoverhangMin 1 \\
+	--outFilterMismatchNmax 999 \\
+	--outFilterMismatchNoverLmax 0.3  \\
+	--alignIntronMin 20 \\
+	--alignIntronMax 1000000 \\
+	--alignMatesGapMax 1000000 \\
+	--readFilesIn {input.R1} \\
+	--readFilesCommand zcat \\
+	--runThreadN {threads} \\
+	--outFileNamePrefix {params.sample}_p1. \\
+	--chimSegmentMin 20 \\
+	--chimMultimapNmax 10 \\
+	--chimOutType Junctions \\
+	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \\
+	--outSAMtype None \\
+	--alignEndsProtrude 10 ConcordantPair \\
+	--outFilterIntronMotifs None \\
+	--sjdbGTFfile {params.gtf} \\
+	--outTmpDir=${{TMPDIR}} \\
 	--sjdbOverhang $overhang
 
 fi
@@ -359,14 +359,14 @@ rule merge_SJ_tabs:
 		filter2_unannotated=config['star1passfilter2_unannotated']
 	threads: 1
 	shell:"""
-cat {input} | \
-python {params.script1} \
-	--regions {params.regions} \
-	--filter1regions {params.filter1regions} \
-	--filter1_noncanonical {params.filter1_noncanonical} \
-	--filter1_unannotated {params.filter1_unannotated} \
-	--filter2_noncanonical {params.filter2_noncanonical} \
-	--filter2_unannotated {params.filter1_unannotated} | \
+cat {input} | \\
+python {params.script1} \\
+	--regions {params.regions} \\
+	--filter1regions {params.filter1regions} \\
+	--filter1_noncanonical {params.filter1_noncanonical} \\
+	--filter1_unannotated {params.filter1_unannotated} \\
+	--filter2_noncanonical {params.filter2_noncanonical} \\
+	--filter2_unannotated {params.filter1_unannotated} | \\
 cut -f1-4 | sort -k1,1 -k2,2n | uniq > {output.pass1sjtab}
 """
 
@@ -405,33 +405,33 @@ if [ "{params.peorse}" == "PE" ];then
 	overhang=$(zcat {input.R1} {input.R2} | awk -v maxlen=100 'NR%4==2 {{if (length($1) > maxlen+0) maxlen=length($1)}}; END {{print maxlen-1}}')
 	echo "sjdbOverhang for STAR: ${{overhang}}"
 	cd {params.outdir}
-	STAR --genomeDir {params.starindexdir} \
-	--outSAMstrandField None  \
-	--outFilterType BySJout \
-	--outFilterMultimapNmax 20 \
-	--alignSJoverhangMin 8 \
-	--alignSJDBoverhangMin 1 \
-	--outFilterMismatchNmax 999 \
-	--outFilterMismatchNoverLmax 0.3  \
-	--alignIntronMin 20 \
-	--alignIntronMax 2000000 \
-	--alignMatesGapMax 2000000 \
-	--readFilesIn {input.R1} {input.R2} \
-	--readFilesCommand  zcat \
-	--runThreadN 56 \
-	--outFileNamePrefix {params.sample}_p2. \
-	--sjdbFileChrStartEnd {input.pass1sjtab} \
-	--chimSegmentMin 20 \
-	--chimOutType Junctions WithinBAM \
-	--chimMultimapNmax 10 \
-	--limitSjdbInsertNsj $limitSjdbInsertNsj \
-	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \
-	--outSAMtype BAM SortedByCoordinate \
-	--alignEndsProtrude 10 ConcordantPair \
-	--outFilterIntronMotifs None \
-	--sjdbGTFfile {params.gtf} \
-	--quantMode GeneCounts \
-	--outTmpDir=${{TMPDIR}} \
+	STAR --genomeDir {params.starindexdir} \\
+	--outSAMstrandField None  \\
+	--outFilterType BySJout \\
+	--outFilterMultimapNmax 20 \\
+	--alignSJoverhangMin 8 \\
+	--alignSJDBoverhangMin 1 \\
+	--outFilterMismatchNmax 999 \\
+	--outFilterMismatchNoverLmax 0.3  \\
+	--alignIntronMin 20 \\
+	--alignIntronMax 2000000 \\
+	--alignMatesGapMax 2000000 \\
+	--readFilesIn {input.R1} {input.R2} \\
+	--readFilesCommand  zcat \\
+	--runThreadN 56 \\
+	--outFileNamePrefix {params.sample}_p2. \\
+	--sjdbFileChrStartEnd {input.pass1sjtab} \\
+	--chimSegmentMin 20 \\
+	--chimOutType Junctions WithinBAM \\
+	--chimMultimapNmax 10 \\
+	--limitSjdbInsertNsj $limitSjdbInsertNsj \\
+	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \\
+	--outSAMtype BAM SortedByCoordinate \\
+	--alignEndsProtrude 10 ConcordantPair \\
+	--outFilterIntronMotifs None \\
+	--sjdbGTFfile {params.gtf} \\
+	--quantMode GeneCounts \\
+	--outTmpDir=${{TMPDIR}} \\
 	--sjdbOverhang $overhang
 
 else
@@ -439,33 +439,33 @@ else
 	overhang=$(zcat {input.R1} | awk -v maxlen=100 'NR%4==2 {{if (length($1) > maxlen+0) maxlen=length($1)}}; END {{print maxlen-1}}')
 	echo "sjdbOverhang for STAR: ${{overhang}}"
 	cd {params.outdir}
-	STAR --genomeDir {params.starindexdir} \
-	--outSAMstrandField None  \
-	--outFilterType BySJout \
-	--outFilterMultimapNmax 20 \
-	--alignSJoverhangMin 8 \
-	--alignSJDBoverhangMin 1 \
-	--outFilterMismatchNmax 999 \
-	--outFilterMismatchNoverLmax 0.3  \
-	--alignIntronMin 20 \
-	--alignIntronMax 2000000 \
-	--alignMatesGapMax 2000000 \
-	--readFilesIn {input.R1} \
-	--readFilesCommand  zcat \
-	--runThreadN 56 \
-	--outFileNamePrefix {params.sample}_p2. \
-	--sjdbFileChrStartEnd {input.pass1sjtab} \
-	--chimSegmentMin 20 \
-	--chimOutType Junctions WithinBAM \
-	--chimMultimapNmax 10 \
-	--limitSjdbInsertNsj $limitSjdbInsertNsj \
-	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \
-	--outSAMtype BAM SortedByCoordinate \
-	--alignEndsProtrude 10 ConcordantPair \
-	--outFilterIntronMotifs None \
-	--sjdbGTFfile {params.gtf} \
-	--quantMode GeneCounts \
-	--outTmpDir=${{TMPDIR}} \
+	STAR --genomeDir {params.starindexdir} \\
+	--outSAMstrandField None  \\
+	--outFilterType BySJout \\
+	--outFilterMultimapNmax 20 \\
+	--alignSJoverhangMin 8 \\
+	--alignSJDBoverhangMin 1 \\
+	--outFilterMismatchNmax 999 \\
+	--outFilterMismatchNoverLmax 0.3  \\
+	--alignIntronMin 20 \\
+	--alignIntronMax 2000000 \\
+	--alignMatesGapMax 2000000 \\
+	--readFilesIn {input.R1} \\
+	--readFilesCommand  zcat \\
+	--runThreadN 56 \\
+	--outFileNamePrefix {params.sample}_p2. \\
+	--sjdbFileChrStartEnd {input.pass1sjtab} \\
+	--chimSegmentMin 20 \\
+	--chimOutType Junctions WithinBAM \\
+	--chimMultimapNmax 10 \\
+	--limitSjdbInsertNsj $limitSjdbInsertNsj \\
+	--alignTranscriptsPerReadNmax {params.alignTranscriptsPerReadNmax} \\
+	--outSAMtype BAM SortedByCoordinate \\
+	--alignEndsProtrude 10 ConcordantPair \\
+	--outFilterIntronMotifs None \\
+	--sjdbGTFfile {params.gtf} \\
+	--quantMode GeneCounts \\
+	--outTmpDir=${{TMPDIR}} \\
 	--sjdbOverhang $overhang
 fi
 ## ensure the star2p file is indexed ... is should already be sorted by STAR
@@ -712,16 +712,16 @@ if [ ! -d {params.outdir} ];then mkdir {params.outdir};fi
 cd {params.outdir}
 mv {input.junctionfile} {input.junctionfile}.original
 grep -v junction_type {input.junctionfile}.original > {input.junctionfile}
-CIRCexplorer2 parse \
-	-t STAR \
+CIRCexplorer2 parse \\
+	-t STAR \\
 	{input.junctionfile} > {params.sample}_circexplorer_parse.log 2>&1
 mv back_spliced_junction.bed {output.backsplicedjunctions}
 mv {input.junctionfile}.original {input.junctionfile}
-CIRCexplorer2 annotate \
--r {params.genepred} \
--g {params.reffa} \
--b {output.backsplicedjunctions} \
--o $(basename {output.annotations}) \
+CIRCexplorer2 annotate \\
+-r {params.genepred} \\
+-g {params.reffa} \\
+-b {output.backsplicedjunctions} \\
+-o $(basename {output.annotations}) \\
 --low-confidence
 """
 
@@ -750,22 +750,22 @@ rule ciri:
 cd {params.outdir}
 if [ "{params.peorse}" == "PE" ];then
 	## paired-end
-	bwa mem -t {threads} -T 19 \
-	{params.bwaindex} \
-	{input.R1} {input.R2} \
+	bwa mem -t {threads} -T 19 \\
+	{params.bwaindex} \\
+	{input.R1} {input.R2} \\
 	> {params.sample}.bwa.sam 2> {output.bwalog}
 else
 	## single-end
-	bwa mem -t {threads} -T 19 \
-	{params.bwaindex} \
-	{input.R1} \
+	bwa mem -t {threads} -T 19 \\
+	{params.bwaindex} \\
+	{input.R1} \\
 	> {params.sample}.bwa.sam 2> {output.bwalog}
 fi
-perl {params.ciripl} \
--I {params.sample}.bwa.sam \
--O {output.ciriout} \
--F {params.reffa} \
--A {params.gtf} \
+perl {params.ciripl} \\
+-I {params.sample}.bwa.sam \\
+-O {output.ciriout} \\
+-F {params.reffa} \\
+-A {params.gtf} \\
 -G {output.cirilog} -T {threads}
 samtools view -@{threads} -bS {params.sample}.bwa.sam > {output.ciribam}
 rm -rf {params.sample}.bwa.sam
@@ -815,11 +815,11 @@ rule clear:
 	container: "docker://nciccbr/ccbr_clear:latest"
 	threads: 4
 	shell:"""
-circ_quant \
--c {input.circexplorerout} \
--b {input.bam} \
--t \
--r {params.genepred} \
+circ_quant \\
+-c {input.circexplorerout} \\
+-b {input.bam} \\
+-t \\
+-r {params.genepred} \\
 -o {output.quantfile}
 """
 
@@ -835,10 +835,15 @@ rule annotate_clear_output:
 	shell:"""
 ## cleanup quant.txt* dirs before annotation
 find {params.cleardir} -maxdepth 1 -type d -name "quant.txt*" -exec rm -rf {{}} \;
+if [[ "$(cat {input.quantfile} | wc -l)" != "0" ]]
+then
 python {params.script} {params.lookup} {input.quantfile}
+else
+touch {output.annotatedquantfile}
+fi
 """		
 
-
+localrules: venn
 rule venn:
 	input:
 		circexplorerout=rules.annotate_circRNA.output.annotations,
@@ -857,16 +862,25 @@ rule venn:
 	shell:"""
 cut -f1 {input.ciriout}|grep -v circRNA_ID > /dev/shm/{params.sample}.ciri.lst
 cut -f1-3 {input.circexplorerout}|awk -F"\\t" '{{print $1\":\"$2+1\"|\"$3}}' > /dev/shm/{params.sample}.circExplorer.lst
-2set_venn.R \
-	-l /dev/shm/{params.sample}.ciri.lst \
-	-r /dev/shm/{params.sample}.circExplorer.lst  \
-	-p {output.png} \
-	-m {output.cirionly} \
-	-s {output.circexploreronly} \
-	-c1 "CIRI2" \
-	-c2 "CircExplorer2" \
-	-c {output.common} \
-	-t {params.sample}
+if [[ "$(cat /dev/shm/{params.sample}.ciri.lst | wc -l)" != "0" ]];then
+	if [[ "$(cat /dev/shm/{params.sample}.circExplorer.lst | wc -l)" != "0" ]];then
+		2set_venn.R \\
+			-l /dev/shm/{params.sample}.ciri.lst \\
+			-r /dev/shm/{params.sample}.circExplorer.lst  \\
+			-p {output.png} \\
+			-m {output.cirionly} \\
+			-s {output.circexploreronly} \\
+			-c1 "CIRI2" \\
+			-c2 "CircExplorer2" \\
+			-c {output.common} \\
+			-t {params.sample}
+	else
+		for o in {output}
+		do
+			touch $o
+		done
+	fi
+fi
 rm -f /dev/shm{params.sample}*
 """