diff --git a/workflow/rules/findcircrna.smk b/workflow/rules/findcircrna.smk
index d3be18b..8a832f7 100644
--- a/workflow/rules/findcircrna.smk
+++ b/workflow/rules/findcircrna.smk
@@ -1354,185 +1354,6 @@ bash {output.merge_bash_script}
 """
 
 
-# if RUN_DCC and RUN_MAPSPLICE and RUN_NCLSCAN:
-#     rule merge_per_sample:
-#         input:
-#             unpack(get_per_sample_files_to_merge)
-#         output:
-#             merged_counts=join(WORKDIR,"results","{sample}","{sample}.circRNA_counts.txt.gz"),
-#         params:
-#             script=join(SCRIPTS_DIR,"_merge_per_sample_counts_table.py"),
-#             samplename="{sample}",
-#             peorse=get_peorse,
-#             reffa=REF_FA,
-#             minreadcount=config['minreadcount'] # this filter is redundant as inputs are already pre-filtered.
-#         envmodules:
-#             TOOLS["python37"]["version"]
-#         shell:"""
-#     set -exo pipefail
-#     outdir=$(dirname {output.merged_counts})
-
-#     parameters=" --circExplorer {input.circExplorer}"
-#     parameters="$parameters --ciri {input.CIRI}"
-#     parameters="$parameters --dcc {input.DCC}"
-#     parameters="$parameters --mapsplice {input.MapSplice}"
-#     if [[ "{params.peorse}" == "PE" ]]; then    # NCLscan is run only if the sample is PE
-#         parameters="$parameters --nclscan {input.NCLscan}"
-#     fi
-#     parameters="$parameters --min_read_count_reqd {params.minreadcount}"
-#     parameters="$parameters --reffa {params.reffa}"
-#     parameters="$parameters --samplename {params.samplename} -o {output.merged_counts}"
-
-#     echo "python {params.script} $parameters"
-#     python {params.script} $parameters
-#     """
-# elif RUN_DCC and not RUN_MAPSPLICE and not RUN_NCLSCAN:
-#     rule merge_per_sample:
-#         input:
-#             unpack(get_per_sample_files_to_merge)
-#         output:
-#             merged_counts=join(WORKDIR,"results","{sample}","{sample}.circRNA_counts.txt.gz"),
-#         params:
-#             script=join(SCRIPTS_DIR,"_merge_per_sample_counts_table.py"),
-#             samplename="{sample}",
-#             peorse=get_peorse,
-#             reffa=REF_FA,
-#             minreadcount=config['minreadcount'] # this filter is redundant as inputs are already pre-filtered.
-#         envmodules:
-#             TOOLS["python37"]["version"]
-#         shell:"""
-#     set -exo pipefail
-#     outdir=$(dirname {output.merged_counts})
-
-#     parameters=" --circExplorer {input.circExplorer}"
-#     parameters="$parameters --ciri {input.CIRI}"
-#     parameters="$parameters --dcc {input.DCC}"
-#     parameters="$parameters --min_read_count_reqd {params.minreadcount}"
-#     parameters="$parameters --reffa {params.reffa}"
-#     parameters="$parameters --samplename {params.samplename} -o {output.merged_counts}"
-
-#     echo "python {params.script} $parameters"
-#     python {params.script} $parameters
-#     """
-# elif RUN_DCC and RUN_MAPSPLICE and not RUN_NCLSCAN:
-#     rule merge_per_sample:
-#         input:
-#             unpack(get_per_sample_files_to_merge)
-#         output:
-#             merged_counts=join(WORKDIR,"results","{sample}","{sample}.circRNA_counts.txt.gz"),
-#         params:
-#             script=join(SCRIPTS_DIR,"_merge_per_sample_counts_table.py"),
-#             samplename="{sample}",
-#             peorse=get_peorse,
-#             reffa=REF_FA,
-#             minreadcount=config['minreadcount'] # this filter is redundant as inputs are already pre-filtered.
-#         envmodules:
-#             TOOLS["python37"]["version"]
-#         shell:"""
-#     set -exo pipefail
-#     outdir=$(dirname {output.merged_counts})
-
-#     parameters=" --circExplorer {input.circExplorer}"
-#     parameters="$parameters --ciri {input.CIRI}"
-#     parameters="$parameters --dcc {input.DCC}"
-#     parameters="$parameters --mapsplice {input.MapSplice}"
-#     parameters="$parameters --min_read_count_reqd {params.minreadcount}"
-#     parameters="$parameters --reffa {params.reffa}"
-#     parameters="$parameters --samplename {params.samplename} -o {output.merged_counts}"
-
-#     echo "python {params.script} $parameters"
-#     python {params.script} $parameters
-#     """
-# elif not RUN_DCC and RUN_MAPSPLICE and not RUN_NCLSCAN:
-#     rule merge_per_sample:
-#         input:
-#             unpack(get_per_sample_files_to_merge)
-#         output:
-#             merged_counts=join(WORKDIR,"results","{sample}","{sample}.circRNA_counts.txt.gz"),
-#         params:
-#             script=join(SCRIPTS_DIR,"_merge_per_sample_counts_table.py"),
-#             samplename="{sample}",
-#             peorse=get_peorse,
-#             reffa=REF_FA,
-#             minreadcount=config['minreadcount'] # this filter is redundant as inputs are already pre-filtered.
-#         envmodules:
-#             TOOLS["python37"]["version"]
-#         shell:"""
-#     set -exo pipefail
-#     outdir=$(dirname {output.merged_counts})
-
-#     parameters=" --circExplorer {input.circExplorer}"
-#     parameters="$parameters --ciri {input.CIRI}"
-#     parameters="$parameters --mapsplice {input.MapSplice}"
-#     parameters="$parameters --min_read_count_reqd {params.minreadcount}"
-#     parameters="$parameters --reffa {params.reffa}"
-#     parameters="$parameters --samplename {params.samplename} -o {output.merged_counts}"
-
-#     echo "python {params.script} $parameters"
-#     python {params.script} $parameters
-#     """
-# elif not RUN_DCC and not RUN_MAPSPLICE and RUN_NCLSCAN:
-#     rule merge_per_sample:
-#         input:
-#             unpack(get_per_sample_files_to_merge)
-#         output:
-#             merged_counts=join(WORKDIR,"results","{sample}","{sample}.circRNA_counts.txt.gz"),
-#         params:
-#             script=join(SCRIPTS_DIR,"_merge_per_sample_counts_table.py"),
-#             samplename="{sample}",
-#             peorse=get_peorse,
-#             reffa=REF_FA,
-#             minreadcount=config['minreadcount'] # this filter is redundant as inputs are already pre-filtered.
-#         envmodules:
-#             TOOLS["python37"]["version"]
-#         shell:"""
-#     set -exo pipefail
-#     outdir=$(dirname {output.merged_counts})
-
-#     parameters=" --circExplorer {input.circExplorer}"
-#     parameters="$parameters --ciri {input.CIRI}"
-#     if [[ "{params.peorse}" == "PE" ]]; then    # NCLscan is run only if the sample is PE
-#         parameters="$parameters --nclscan {input.NCLscan}"
-#     fi
-#     parameters="$parameters --min_read_count_reqd {params.minreadcount}"
-#     parameters="$parameters --reffa {params.reffa}"
-#     parameters="$parameters --samplename {params.samplename} -o {output.merged_counts}"
-
-#     echo "python {params.script} $parameters"
-#     python {params.script} $parameters
-#     """
-# else: # DCC, MapSplice and NCLScan are all off!
-#     rule merge_per_sample:
-#         input:
-#             unpack(get_per_sample_files_to_merge)
-#         output:
-#             merged_counts=join(WORKDIR,"results","{sample}","{sample}.circRNA_counts.txt.gz"),
-#         params:
-#             script=join(SCRIPTS_DIR,"_merge_per_sample_counts_table.py"),
-#             samplename="{sample}",
-#             peorse=get_peorse,
-#             reffa=REF_FA,
-#             minreadcount=config['minreadcount'] # this filter is redundant as inputs are already pre-filtered.
-#         envmodules:
-#             TOOLS["python37"]["version"]
-#         shell:"""
-#     set -exo pipefail
-#     outdir=$(dirname {output.merged_counts})
-
-#     parameters=" --circExplorer {input.circExplorer}"
-#     parameters="$parameters --ciri {input.CIRI}"
-#     parameters="$parameters --min_read_count_reqd {params.minreadcount}"
-#     parameters="$parameters --reffa {params.reffa}"
-#     parameters="$parameters --samplename {params.samplename} -o {output.merged_counts}"
-
-#     echo "python {params.script} $parameters"
-#     python {params.script} $parameters
-#     """
-
-
-# localrules:
-#     create_master_counts_file,
-
 
 # rule create_master_counts_file:
 # merge all per-sample counts tables into a single giant counts matrix and annotate it with known circRNA databases
diff --git a/workflow/rules/post_align_processing.smk b/workflow/rules/post_align_processing.smk
index faea673..21b0bc5 100644
--- a/workflow/rules/post_align_processing.smk
+++ b/workflow/rules/post_align_processing.smk
@@ -1,92 +1,3 @@
-# rule split_splice_reads_BAM_create_BW:
-#     input:
-#         bam=rules.create_spliced_reads_bam.output.bam
-#     output:
-#         bam=join(WORKDIR,"results","{sample}","STAR2p","{sample}.spliced_reads."+HOST+".bam"),
-#         bw=join(WORKDIR,"results","{sample}","STAR2p","{sample}.spliced_reads."+HOST+".bw")
-#     params:
-#         sample="{sample}",
-#         workdir=WORKDIR,
-#         memG=getmemG("split_splice_reads_BAM_create_BW"),
-#         outdir=join(WORKDIR,"results","{sample}","STAR2p"),
-#         regions=REF_REGIONS,
-#         randomstr=str(uuid.uuid4())
-#     threads: getthreads("split_splice_reads_BAM_create_BW")
-#     envmodules: TOOLS["samtools"]["version"],TOOLS["bedtools"]["version"],TOOLS["ucsc"]["version"],TOOLS["sambamba"]["version"]
-#     shell:"""
-# if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-#     TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-# else
-#     TMPDIR="/dev/shm/{params.randomstr}"
-#     mkdir -p $TMPDIR
-# fi
-# cd {params.outdir}
-# bam_basename="$(basename {input.bam})"
-# while read a b;do
-# bam="${{bam_basename%.*}}.${{a}}.bam"
-# samtools view {input.bam} $b -b > ${{TMPDIR}}/${{bam%.*}}.tmp.bam
-# sambamba sort --memory-limit={params.memG} --tmpdir=${{TMPDIR}} --nthreads={threads} --out=$bam ${{TMPDIR}}/${{bam%.*}}.tmp.bam
-# bw="${{bam%.*}}.bw"
-# bdg="${{bam%.*}}.bdg"
-# sizes="${{bam%.*}}.sizes"
-# bedtools genomecov -bga -split -ibam $bam > $bdg
-# bedSort $bdg $bdg
-# if [ "$(wc -l $bdg|awk '{{print $1}}')" != "0" ];then
-# samtools view -H $bam|grep ^@SQ|cut -f2,3|sed "s/SN://g"|sed "s/LN://g" > $sizes
-# bedGraphToBigWig $bdg $sizes $bw
-# else
-# touch $bw
-# fi
-# rm -f $bdg $sizes
-# done < {params.regions}
-# cd $TMPDIR && rm -f *
-# """
-
-# rule split_linear_reads_BAM_create_BW:
-# # This rule is identical to split_splice_reads_BAM_create_BW, "spliced_reads" is replaced by "linear_reads"
-#     input:
-#         bam=rules.create_linear_reads_bam.output.bam
-#     output:
-#         bam=join(WORKDIR,"results","{sample}","STAR2p","{sample}.linear_reads."+HOST+".bam"),
-#         bw=join(WORKDIR,"results","{sample}","STAR2p","{sample}.linear_reads."+HOST+".bw")
-#     params:
-#         sample="{sample}",
-#         workdir=WORKDIR,
-#         memG=getmemG("split_linear_reads_BAM_create_BW"),
-#         outdir=join(WORKDIR,"results","{sample}","STAR2p"),
-#         regions=REF_REGIONS,
-#         randomstr=str(uuid.uuid4())
-#     threads: getthreads("split_linear_reads_BAM_create_BW")
-#     envmodules: TOOLS["samtools"]["version"],TOOLS["bedtools"]["version"],TOOLS["ucsc"]["version"],TOOLS["sambamba"]["version"]
-#     shell:"""
-# if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-#     TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-# else
-#     TMPDIR="/dev/shm/{params.randomstr}"
-#     mkdir -p $TMPDIR
-# fi
-# cd {params.outdir}
-# bam_basename="$(basename {input.bam})"
-# while read a b;do
-# bam="${{bam_basename%.*}}.${{a}}.bam"
-# samtools view {input.bam} $b -b > ${{TMPDIR}}/${{bam%.*}}.tmp.bam
-# sambamba sort --memory-limit={params.memG} --tmpdir=${{TMPDIR}} --nthreads={threads} --out=$bam ${{TMPDIR}}/${{bam%.*}}.tmp.bam
-# bw="${{bam%.*}}.bw"
-# bdg="${{bam%.*}}.bdg"
-# sizes="${{bam%.*}}.sizes"
-# bedtools genomecov -bga -split -ibam $bam > $bdg
-# bedSort $bdg $bdg
-# if [ "$(wc -l $bdg|awk '{{print $1}}')" != "0" ];then
-# samtools view -H $bam|grep ^@SQ|cut -f2,3|sed "s/SN://g"|sed "s/LN://g" > $sizes
-# bedGraphToBigWig $bdg $sizes $bw
-# else
-# touch $bw
-# fi
-# rm -f $bdg $sizes
-# done < {params.regions}
-# cd $TMPDIR && rm -f *
-# """
-
 
 localrules:
     merge_genecounts,
diff --git a/workflow/rules/post_findcircrna_processing.smk b/workflow/rules/post_findcircrna_processing.smk
index 84a0387..908fd9e 100644
--- a/workflow/rules/post_findcircrna_processing.smk
+++ b/workflow/rules/post_findcircrna_processing.smk
@@ -529,224 +529,3 @@ for bam in $(ls {params.samplename}.*.HQ_only.BSJ.bam);do
     fi
 done
 """
-
-
-
-# localrules: venn
-# rule venn:
-#     input:
-#         circexplorerout=rules.circExplorer.output.annotations,
-#         ciriout=rules.ciri.output.cirioutfiltered
-#     output:
-#         png=join(WORKDIR,"results","{sample}","{sample}.venn_mqc.png"),
-#         cirionly=join(WORKDIR,"results","{sample}","{sample}.cirionly.lst"),
-#         circexploreronly=join(WORKDIR,"results","{sample}","{sample}.circexploreronly.lst"),
-#         common=join(WORKDIR,"results","{sample}","{sample}.common.lst")
-#     params:
-#         script1=join(SCRIPTS_DIR,"venn.R"),
-#         sample="{sample}",
-#         outdir=join(WORKDIR,"results","{sample}")
-#     container: "docker://nciccbr/ccbr_venn:latest"
-#     threads: getthreads("venn")
-#     shell:"""
-# set -exo pipefail
-# 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\"|\"$3}}' > /dev/shm/{params.sample}.circExplorer.lst
-# if [[ "$(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 $o
-#         done
-#     fi
-# fi
-# rm -f /dev/shm{params.sample}*
-# """
-
-
-# rule add_strand_to_circExplorer:
-# 	input:
-# 		backsplicedjunctions=rules.circExplorer.output.backsplicedjunctions,
-# 		bed=rules.split_BAM_create_BW.output.bed
-# 	output:
-# 		backsplicedjunctions=join(WORKDIR,"results","{sample}","circExplorer","{sample}.back_spliced_junction.bed"),
-# 	params:
-# 		sample="{sample}",
-# 		workdir=WORKDIR,
-# 		pythonscript=join(SCRIPTS_DIR,"copy_strand_info.py"),
-# 	threads: 2
-# 	# envmodules:
-# 	shell:"""
-# 	cp {input.backsplicedjunctions} /dev/shm
-# 	bsj_basename="$(basename {input.backsplicedjunctions})"
-# 	python {params.pythonscript} --from {input.bed} --to /dev/shm/${{bsj_basename}} --output {output.backsplicedjunctions}
-# """
-
-# rule recall_valid_BSJ_split_BAM_by_strand_create_BW:
-#     input:
-#         bam=rules.create_circExplorer_BSJ_bam.output.BSJbam,
-#     output:
-#         bam=join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ."+HOST+".bam"),
-#         plusbam=join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ."+HOST+".plus.bam"),
-#         minusbam=join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ."+HOST+".minus.bam"),
-#         bed=join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ."+HOST+".bed"),
-#         bw=join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ."+HOST+".bw"),
-#         plusbw=join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ."+HOST+".plus.bw"),
-#         minusbw=join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ."+HOST+".minus.bw"),
-#         validBSJbed=join(WORKDIR,"results","{sample}","customBSJs","{sample}.valid_STAR_BSJ.bed")
-#     params:
-#         sample="{sample}",
-#         workdir=WORKDIR,
-#         memG=getmemG("recall_valid_BSJ_split_BAM_by_strand_create_BW"),
-#         outdir=join(WORKDIR,"results","{sample}","STAR2p","BSJs"),
-#         pythonscript=join(SCRIPTS_DIR,"validate_BSJ_reads_and_split_BSJ_bam_by_strand.py"),
-#         regions=REF_REGIONS,
-#         randomstr=str(uuid.uuid4())
-#     threads: getthreads("recall_valid_BSJ_split_BAM_by_strand_create_BW")
-#     envmodules: TOOLS["samtools"]["version"],TOOLS["bedtools"]["version"],TOOLS["ucsc"]["version"],TOOLS["sambamba"]["version"],TOOLS["python37"]["version"]
-#     shell:"""
-# set -exo pipefail
-# if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-#     TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-# else
-#     TMPDIR="/dev/shm/{params.randomstr}"
-#     mkdir -p $TMPDIR
-# fi
-# cd {params.outdir}
-# bam_basename="$(basename {input.bam})"
-# while read a b;do
-# bam="${{bam_basename%.*}}.${{a}}.bam"
-# plusbam="${{bam_basename%.*}}.${{a}}.plus.bam"
-# minusbam="${{bam_basename%.*}}.${{a}}.minus.bam"
-# bed="${{bam_basename%.*}}.${{a}}.bed"
-# samtools view {input.bam} $b -b > ${{TMPDIR}}/${{bam%.*}}.tmp.bam
-# sambamba sort --memory-limit={params.memG} --tmpdir=${{TMPDIR}} --nthreads={threads} --out=$bam ${{TMPDIR}}/${{bam%.*}}.tmp.bam
-# bw="${{bam%.*}}.bw"
-# bdg="${{bam%.*}}.bdg"
-# plusbw="${{bam%.*}}.plus.bw"
-# plusbdg="${{bam%.*}}.plus.bdg"
-# minusbw="${{bam%.*}}.minus.bw"
-# minusbdg="${{bam%.*}}.minus.bdg"
-# sizes="${{bam%.*}}.sizes"
-# # create strand specific bams
-# python {params.pythonscript} \
-# -i $bam \
-# -p $plusbam \
-# -m $minusbam \
-# -b $bed
-# bedSort $bed $bed
-# # create bedgraphs
-# bedtools genomecov -bga -split -ibam $bam > $bdg
-# bedSort $bdg $bdg
-# bedtools genomecov -bga -split -ibam $plusbam > $plusbdg
-# bedSort $plusbdg $plusbdg
-# bedtools genomecov -bga -split -ibam $minusbam > $minusbdg
-# bedSort $minusbdg $minusbdg
-# # create bigwigs
-# if [ "$(wc -l $bdg|awk '{{print $1}}')" != "0" ];then
-#     samtools view -H $bam|grep ^@SQ|cut -f2,3|sed "s/SN://g"|sed "s/LN://g" > $sizes
-#     bedGraphToBigWig $bdg $sizes $bw
-#     if [ "$(wc -l $plusbdg|awk '{{print $1}}')" != "0" ];then
-#         bedGraphToBigWig $plusbdg $sizes $plusbw
-#     else
-#         touch $plusbw
-#     fi
-#     if [ "$(wc -l $minusbdg|awk '{{print $1}}')" != "0" ];then
-#         bedGraphToBigWig $minusbdg $sizes $minusbw
-#     else
-#         touch $minusbw
-#     fi
-# else
-#     touch $bw
-# fi
-# rm -f $bdg $sizes
-
-# done < {params.regions}
-# cat {params.sample}.BSJ.*.bed |cut -f1-6 > ${{TMPDIR}}/{sample}.tmp.bed
-# bedSort ${{TMPDIR}}/{sample}.tmp.bed ${{TMPDIR}}/{sample}.tmp.bed
-# awk -F"\\t" -v OFS="\\t" '{{$4="S"NR;print}}' ${{TMPDIR}}/{sample}.tmp.bed > {output.validBSJbed}
-# cd $TMPDIR && rm -f *
-# """
-
-# rule add_novel_ciri_BSJs_to_customBSJ:
-#     input:
-#         ciriout=rules.ciri.output.ciriout,
-#         hg38bed=rules.recall_valid_BSJ_split_BAM_by_strand_create_BW.output.bed,
-#         validBSJbed=rules.recall_valid_BSJ_split_BAM_by_strand_create_BW.output.validBSJbed,
-#     output:
-#         novelBSJ=join(WORKDIR,"results","{sample}","customBSJs","{sample}.novel_CIRI_BSJ.bed"),
-#         cirireadids=temp(join(WORKDIR,"results","{sample}","customBSJs","{sample}.ciri.readids")),
-#         combinedBSJ=join(WORKDIR,"results","{sample}","customBSJs","{sample}.BSJ.bed")
-#     params:
-#         sample="{sample}",
-#         outdir=join(WORKDIR,"results","{sample}","customBSJs"),
-#         list_compare_script=join(SCRIPTS_DIR,"_compare_lists.py"),
-#         randomstr=str(uuid.uuid4())
-#     envmodules: TOOLS["ucsc"]["version"],TOOLS["python37"]["version"]
-#     shell:"""
-# set -exo pipefail
-# if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-#     TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-# else
-#     TMPDIR="/dev/shm/{params.randomstr}"
-#     mkdir -p $TMPDIR
-# fi
-# cd {params.outdir}
-# grep -v junction_reads_ID {input.ciriout}|awk -F"\\t" '{{print substr($NF,1,length($NF)-1)}}'|tr ',' '\\n'|sort|uniq > {params.sample}.ciri.readids
-# stardir=$(dirname {input.hg38bed})
-# cat ${{stardir}}/{params.sample}.BSJ.*.bed|awk -F"\\t" '{{print $NF}}'|tr ',' '\\n'|awk -F"##" '{{print $1}}'|sort|uniq > {params.sample}.circExplorer.readids
-# python {params.list_compare_script} {params.sample}.ciri.readids {params.sample}.circExplorer.readids 1
-# mv a_only.lst {params.sample}.ciri.novel.readids && rm -f a_* b_*
-# head -n1 {input.ciriout} > {params.sample}.ciri.novel.out
-# while read a;do grep $a {input.ciriout};done < {params.sample}.ciri.novel.readids |sort|uniq >> {params.sample}.ciri.novel.out
-# grep -v circRNA_ID {params.sample}.ciri.novel.out | awk -F"\\t" -v OFS="\\t" '{{print $2,$3-1,$4,$2":"$3-1"-"$4,$5,$11}}'  > ${{TMPDIR}}/{params.sample}.novel_CIRI_BSJ.tmp.bed
-# awk -F"\\t" '{{print $4}}' ${{TMPDIR}}/{params.sample}.novel_CIRI_BSJ.tmp.bed > ${{TMPDIR}}/{params.sample}.novel_CIRI_BSJ.tmp.lst
-# awk -F"\\t" '{{print $1":"$2"-"$3}}' {input.validBSJbed} > ${{TMPDIR}}/{params.sample}.circExplorer.BSJ.lst
-# python {params.list_compare_script} ${{TMPDIR}}/{params.sample}.novel_CIRI_BSJ.tmp.lst ${{TMPDIR}}/{params.sample}.circExplorer.BSJ.lst 1
-# mv a_only.lst {params.sample}.ciri.novel.BSJ.lst && rm -f a_* b_*
-# while read a;do grep $a ${{TMPDIR}}/{params.sample}.novel_CIRI_BSJ.tmp.bed;done < {params.sample}.ciri.novel.BSJ.lst > ${{TMPDIR}}/{params.sample}.ciri.novel.BSJ.bed
-# bedSort ${{TMPDIR}}/{params.sample}.ciri.novel.BSJ.bed ${{TMPDIR}}/{params.sample}.ciri.novel.BSJ.bed
-# awk -F"\\t" -v OFS="\\t" '{{$4="C"NR;print}}' ${{TMPDIR}}/{params.sample}.ciri.novel.BSJ.bed > {output.novelBSJ}
-# cat {input.validBSJbed} {output.novelBSJ} > {output.combinedBSJ}
-# bedSort {output.combinedBSJ} {output.combinedBSJ}
-# rm -f {params.sample}.circExplorer.readids {params.sample}.ciri.novel.*
-# cd $TMPDIR && rm -f *
-# """
-# rule filter_ciri_bam_for_BSJs:
-#     input:
-#         bam=rules.ciri.output.ciribam,
-#         ciriout=rules.ciri.output.cirioutfiltered,
-#         readids=rules.add_novel_ciri_BSJs_to_customBSJ.output.cirireadids
-#     output:
-#         bam=join(WORKDIR,"results","{sample}","ciri","{sample}.bwa.BSJ.bam")
-#     params:
-#         sample="{sample}",
-#         memG=getmemG("filter_ciri_bam_for_BSJs"),
-#         script=join(SCRIPTS_DIR,"filter_bam_by_readids.py"),
-#         randomstr=str(uuid.uuid4())
-#     threads: getthreads("filter_ciri_bam_for_BSJs")
-#     envmodules: TOOLS["python37"]["version"],TOOLS["sambamba"]["version"]
-#     shell:"""
-# set -exo pipefail
-# if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-#     TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-# else
-#     TMPDIR="/dev/shm/{params.randomstr}"
-#     mkdir -p $TMPDIR
-# fi
-# sambamba sort --memory-limit={params.memG} --tmpdir=${{TMPDIR}} --nthreads={threads} --out=${{TMPDIR}}/{params.sample}.ciri.sorted.bam {input.bam}
-# python {params.script} --inputBAM ${{TMPDIR}}/{params.sample}.ciri.sorted.bam --outputBAM ${{TMPDIR}}/{params.sample}.tmp.bam --readids {input.readids}
-# sambamba sort --memory-limit={params.memG} --tmpdir=${{TMPDIR}} --nthreads={threads} --out={output.bam} ${{TMPDIR}}/{params.sample}.tmp.bam
-# cd $TMPDIR && rm -f *
-# """