diff --git a/CHANGELOG.md b/CHANGELOG.md
index d2968ae..d35c400 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 - Major updates to convert CHARLIE from a biowulf-specific to a platform-agnostic pipeline (#102, @kelly-sovacool):
     - All rules now use containers instead of envmodules.
     - Default config and cluster config files are provided for use on biowulf and FRCE.
+    - New entry `TEMPDIR` in the config file sets the temporary directory location for rules that require transient storage.
 
 # CHARLIE 0.10.1
 
diff --git a/config/biowulf/config.yaml b/config/biowulf/config.yaml
index 4635749..da1eb19 100644
--- a/config/biowulf/config.yaml
+++ b/config/biowulf/config.yaml
@@ -2,30 +2,32 @@
 #
 # The working dir... output will be in the results subfolder of the workdir
 workdir: "WORKDIR"
-#
+
+# temporary directory for intermediate files that are not saved
+tempdir: '/lscratch/$SLURM_JOB_ID'
+
 # tab delimited samples file ... should have the following 3 columns
 # sampleName	path_to_R1_fastq	path_to_R2_fastq
-#
 samples: "WORKDIR/samples.tsv"
-#
+
 # Should the CLEAR pipeline be run? True or False WITHOUT quotes
 run_clear: True
-#
+
 # Should the DCC pipeline be run? True or False WITHOUT quote
 run_dcc: True
-#
+
 # Should the MapSplice pipeline be run? True or False WITHOUT quotes
 run_mapsplice: False
 mapsplice_min_map_len: 50
 mapsplice_filtering: 2 # 1=less stringent 2=default
-#
+
 # Should the circRNA_finder  be run? True or False WITHOUT quotes
 run_circRNAFinder: True
 # Should the NCLscan pipeline be run? True or False WITHOUT quotes
 # This can only be run for PE data
 run_nclscan: False
 nclscan_config: "WORKDIR/nclscan.config"
-#
+
 # Should we also run find_circ? True or False WITHOUT quotes
 run_findcirc: False
 # findcirc_params: "--noncanonical --allhits" # this gives way too many circRNAs
diff --git a/config/fnlcr/config.yaml b/config/fnlcr/config.yaml
index ecea5a1..5f89a8f 100644
--- a/config/fnlcr/config.yaml
+++ b/config/fnlcr/config.yaml
@@ -2,30 +2,32 @@
 #
 # The working dir... output will be in the results subfolder of the workdir
 workdir: "WORKDIR"
-#
+
+# temporary directory for intermediate files that are not saved
+tempdir: '/scratch/local'
+
 # tab delimited samples file ... should have the following 3 columns
 # sampleName	path_to_R1_fastq	path_to_R2_fastq
-#
 samples: "WORKDIR/samples.tsv"
-#
+
 # Should the CLEAR pipeline be run? True or False WITHOUT quotes
 run_clear: True
-#
+
 # Should the DCC pipeline be run? True or False WITHOUT quote
 run_dcc: True
-#
+
 # Should the MapSplice pipeline be run? True or False WITHOUT quotes
 run_mapsplice: False
 mapsplice_min_map_len: 50
 mapsplice_filtering: 2 # 1=less stringent 2=default
-#
+
 # Should the circRNA_finder  be run? True or False WITHOUT quotes
 run_circRNAFinder: True
 # Should the NCLscan pipeline be run? True or False WITHOUT quotes
 # This can only be run for PE data
 run_nclscan: False
 nclscan_config: "WORKDIR/nclscan.config"
-#
+
 # Should we also run find_circ? True or False WITHOUT quotes
 run_findcirc: False
 # findcirc_params: "--noncanonical --allhits" # this gives way too many circRNAs
diff --git a/docs/tutorial.md b/docs/tutorial.md
index 2bd761b..158c6fb 100644
--- a/docs/tutorial.md
+++ b/docs/tutorial.md
@@ -174,6 +174,7 @@ The above command creates `<path to output dir>` folder and creates 2 subfolders
 This file is used to fine tune the execution of the pipeline by setting:
 
 * sample sheet location ... aka `samples.tsv`
+* the temporary directory -- make sure this is correct for your computing environment.
 * which circRNA finding tools to use by editing these:
     * run_clear: True
     * run_dcc: True
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
index bbda26c..a690c06 100644
--- a/workflow/rules/align.smk
+++ b/workflow/rules/align.smk
@@ -53,19 +53,12 @@ rule star1p:
         outdir=join(WORKDIR, "results", "{sample}", "STAR1p"),
         starindexdir=STAR_INDEX_DIR,
         alignTranscriptsPerReadNmax=config["alignTranscriptsPerReadNmax"],
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']["star"]
     threads: getthreads("star1p")
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-
-if [ ! -d {params.outdir} ];then mkdir {params.outdir};fi
 if [ "{params.peorse}" == "PE" ];then
 # paired-end
     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}}')
@@ -99,7 +92,7 @@ if [ "{params.peorse}" == "PE" ];then
     --alignEndsProtrude 10 ConcordantPair \\
     --outFilterIntronMotifs None \\
     --sjdbGTFfile {input.gtf} \\
-    --outTmpDir ${{TMPDIR}} \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbOverhang $overhang
 
     rm -rf {params.sample}_p1._STARgenome
@@ -135,7 +128,7 @@ if [ "{params.peorse}" == "PE" ];then
     --alignEndsProtrude 10 ConcordantPair \\
     --outFilterIntronMotifs None \\
     --sjdbGTFfile {input.gtf} \\
-    --outTmpDir ${{TMPDIR}} \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbOverhang $overhang
 
     rm -rf {params.sample}_mate1._STARgenome
@@ -171,7 +164,7 @@ if [ "{params.peorse}" == "PE" ];then
     --alignEndsProtrude 10 ConcordantPair \\
     --outFilterIntronMotifs None \\
     --sjdbGTFfile {input.gtf} \\
-    --outTmpDir ${{TMPDIR}} \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbOverhang $overhang
 
     rm -rf {params.sample}_mate2._STARgenome
@@ -211,7 +204,7 @@ else
     --alignEndsProtrude 10 ConcordantPair \\
     --outFilterIntronMotifs None \\
     --sjdbGTFfile {input.gtf} \\
-    --outTmpDir ${{TMPDIR}} \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbOverhang $overhang
     mkdir -p $(dirname {output.mate1_chimeric_junctions})
     touch {output.mate1_chimeric_junctions}
@@ -304,19 +297,13 @@ rule star2p:
         outdir=join(WORKDIR, "results", "{sample}", "STAR2p"),
         starindexdir=STAR_INDEX_DIR,
         alignTranscriptsPerReadNmax=config["alignTranscriptsPerReadNmax"],
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("star2p")
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
 
-if [ ! -d {params.outdir} ];then mkdir {params.outdir};fi
 limitSjdbInsertNsj=$(wc -l {input.pass1sjtab}|awk '{{print $1+1}}')
 if [ "$limitSjdbInsertNsj" -lt "400000" ];then limitSjdbInsertNsj="400000";fi
 
@@ -359,7 +346,7 @@ if [ "{params.peorse}" == "PE" ];then
     --outFilterIntronMotifs None \\
     --sjdbGTFfile {input.gtf} \\
     --quantMode GeneCounts \\
-    --outTmpDir ${{TMPDIR}} \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbOverhang $overhang \\
     --outBAMcompression 0 \\
     --outSAMattributes All
@@ -404,7 +391,7 @@ else
     --outFilterIntronMotifs None \\
     --sjdbGTFfile {input.gtf} \\
     --quantMode GeneCounts \\
-    --outTmpDir ${{TMPDIR}} \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbOverhang $overhang \\
     --outBAMcompression 0 \\
     --outSAMattributes All
@@ -412,35 +399,35 @@ else
     rm -rf ${{output_prefix}}_STARgenome
 fi
 sleep 120
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
-samtools view -H {output.unsortedbam} > ${{TMPDIR}}/{params.sample}_p2.non_chimeric.sam
-cp ${{TMPDIR}}/{params.sample}_p2.non_chimeric.sam ${{TMPDIR}}/{params.sample}_p2.chimeric.sam
+mkdir -p {params.tmpdir}
+samtools view -H {output.unsortedbam} > {params.tmpdir}/{params.sample}_p2.non_chimeric.sam
+cp {params.tmpdir}/{params.sample}_p2.non_chimeric.sam {params.tmpdir}/{params.sample}_p2.chimeric.sam
 # ref https://github.com/alexdobin/STAR/issues/678
-samtools view -@ {threads} {output.unsortedbam} | grep "ch:A:1" >> ${{TMPDIR}}/{params.sample}_p2.chimeric.sam
-samtools view -@ {threads} {output.unsortedbam} | grep -v "ch:A:1" >> ${{TMPDIR}}/{params.sample}_p2.non_chimeric.sam
+samtools view -@ {threads} {output.unsortedbam} | grep "ch:A:1" >> {params.tmpdir}/{params.sample}_p2.chimeric.sam
+samtools view -@ {threads} {output.unsortedbam} | grep -v "ch:A:1" >> {params.tmpdir}/{params.sample}_p2.non_chimeric.sam
 ls -alrth
 for i in 1 2 3;do
-    if [ ! -d ${{TMPDIR}}/{params.randomstr}_${{i}} ];then mkdir -p ${{TMPDIR}}/{params.randomstr}_${{i}};fi
+    mkdir -p {params.tmpdir}_${{i}}
 done
-samtools view -@ {threads} -b -S ${{TMPDIR}}/{params.sample}_p2.chimeric.sam | \\
+samtools view -@ {threads} -b -S {params.tmpdir}/{params.sample}_p2.chimeric.sam | \\
 samtools sort \\
     -l 9 \\
-    -T ${{TMPDIR}}/{params.randomstr}_1 \\
+    -T {params.tmpdir}_1 \\
     --write-index \\
     -@ {threads} \\
     --output-fmt BAM \\
     -o {output.chimeric_bam} -
-samtools view -@ {threads} -b -S ${{TMPDIR}}/{params.sample}_p2.non_chimeric.sam | \\
+samtools view -@ {threads} -b -S {params.tmpdir}/{params.sample}_p2.non_chimeric.sam | \\
 samtools sort \\
     -l 9 \\
-    -T ${{TMPDIR}}/{params.randomstr}_2 \\
+    -T {params.tmpdir}_2 \\
     --write-index \\
     -@ {threads} \\
     --output-fmt BAM \\
     -o {output.non_chimeric_bam} -
 samtools sort \\
     -l 9 \\
-    -T ${{TMPDIR}}/{params.randomstr}_3 \\
+    -T {params.tmpdir}_3 \\
     --write-index \\
     -@ {threads} \\
     --output-fmt BAM \\
@@ -479,17 +466,12 @@ rule star_circrnafinder:
         flanksize=FLANKSIZE,
         starindexdir=STAR_INDEX_DIR,
         alignTranscriptsPerReadNmax=config["alignTranscriptsPerReadNmax"],
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("star_circrnafinder")
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
 
 outdir=$(dirname {output.chimericsam})
 if [ ! -d $outdir ];then mkdir -p $outdir;fi
@@ -514,7 +496,7 @@ if [ "{params.peorse}" == "PE" ];then
     --outFilterMultimapNmax 2 \\
     --outFileNamePrefix {params.sample}. \\
     --outBAMcompression 0 \\
-    --outTmpDir $TMPDIR \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbGTFfile {input.gtf}
 
 else
@@ -536,7 +518,7 @@ else
     --outFilterMultimapNmax 2 \\
     --outFileNamePrefix {params.sample}. \\
     --outBAMcompression 0 \\
-    --outTmpDir $TMPDIR \\
+    --outTmpDir {params.tmpdir} \\
     --sjdbGTFfile {input.gtf}
 
 fi
@@ -571,18 +553,13 @@ rule find_circ_align:
         sample="{sample}",
         reffa=REF_FA,
         peorse=get_peorse,
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("find_circ_align")
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.tmpdir}
 
 refdir=$(dirname {input.bt2})
 outdir=$(dirname {output.anchorsfq})
@@ -598,7 +575,7 @@ bowtie2 \\
     -q \\
     -1 {input.R1} \\
     -2 {input.R2} \\
-    > ${{TMPDIR}}/{params.sample}.sam
+    > {params.tmpdir}/{params.sample}.sam
 else 
 bowtie2 \\
     -p {threads} \\
@@ -608,35 +585,35 @@ bowtie2 \\
     -x ${{refdir}}/ref \\
     -q \\
     -U {input.R1} \\
-    > ${{TMPDIR}}/{params.sample}.sam
+    > {params.tmpdir}/{params.sample}.sam
 fi
 
-samtools view -@{threads} -hbuS -o ${{TMPDIR}}/{params.sample}.unsorted.bam ${{TMPDIR}}/{params.sample}.sam
+samtools view -@{threads} -hbuS -o {params.tmpdir}/{params.sample}.unsorted.bam {params.tmpdir}/{params.sample}.sam
 
 samtools sort -@{threads} \\
     -u \\
     --write-index \\
     --output-fmt BAM \\
-    -T ${{TMPDIR}}/{params.sample}.samtoolssort \\
-    -o ${{TMPDIR}}/{params.sample}.sorted.bam ${{TMPDIR}}/{params.sample}.unsorted.bam
+    -T {params.tmpdir}/{params.sample}.samtoolssort \\
+    -o {params.tmpdir}/{params.sample}.sorted.bam {params.tmpdir}/{params.sample}.unsorted.bam
 
 samtools view -@{threads} \\
     --output-fmt BAM \\
     --write-index \\
-    -o ${{TMPDIR}}/{params.sample}.unmapped.bam \\
+    -o {params.tmpdir}/{params.sample}.unmapped.bam \\
     -f4 \\
-    ${{TMPDIR}}/{params.sample}.sorted.bam
+    {params.tmpdir}/{params.sample}.sorted.bam
 
 unmapped2anchors.py \\
-    ${{TMPDIR}}/{params.sample}.unmapped.bam | \\
-	gzip -c - > ${{TMPDIR}}/{params.sample}.anchors.fastq.gz
+    {params.tmpdir}/{params.sample}.unmapped.bam | \\
+	gzip -c - > {params.tmpdir}/{params.sample}.anchors.fastq.gz
 
-mv ${{TMPDIR}}/{params.sample}.anchors.fastq.gz {output.anchorsfq}
-mv ${{TMPDIR}}/{params.sample}.unmapped.b* ${{outdir}}/
+mv {params.tmpdir}/{params.sample}.anchors.fastq.gz {output.anchorsfq}
+mv {params.tmpdir}/{params.sample}.unmapped.b* ${{outdir}}/
 
 sleep 300 
 
-rm -rf $TMPDIR
+rm -rf {params.tmpdir}
 """
 
 
diff --git a/workflow/rules/create_index.smk b/workflow/rules/create_index.smk
index 8cc4db4..419c036 100644
--- a/workflow/rules/create_index.smk
+++ b/workflow/rules/create_index.smk
@@ -20,7 +20,6 @@ rule create_index:
         script1=join(SCRIPTS_DIR, "_add_geneid2genepred.py"),
         script2=join(SCRIPTS_DIR, "_multifasta2separatefastas.sh"),
         script3=join(SCRIPTS_DIR, "fix_gtfs.py"),
-        randomstr=str(uuid.uuid4()),
         nclscan_config=config["nclscan_config"],
     container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("create_index")
diff --git a/workflow/rules/findcircrna.smk b/workflow/rules/findcircrna.smk
index a9687dd..16d0c10 100644
--- a/workflow/rules/findcircrna.smk
+++ b/workflow/rules/findcircrna.smk
@@ -197,24 +197,18 @@ rule circExplorer:
         minsize_virus=config["minsize_virus"],
         maxsize_virus=config["maxsize_virus"],
         bash_script=join(SCRIPTS_DIR,"_run_circExplorer_star.sh"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
         # script=join(SCRIPTS_DIR, "circExplorer_get_annotated_counts_per_sample.py"),  # this produces an annotated counts table to which counts found in BAMs need to be appended
     threads: getthreads("circExplorer")
     container: config['containers']["circexplorer"]
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
-if [ ! -d {params.outdir} ];then mkdir {params.outdir};fi
+mkdir -p {params.outdir} {params.tmpdir}
 cd {params.outdir}
 bash {params.bash_script} \\
     --junctionfile {input.junctionfile} \\
-    --tmpdir $TMPDIR \\
+    --tmpdir {params.tmpdir} \\
     --outdir {params.outdir} \\
     --samplename {params.sample} \\
     --genepred {params.genepred} \\
@@ -282,18 +276,12 @@ rule ciri:
         minsize_virus=config["minsize_virus"],
         maxsize_virus=config["maxsize_virus"],
         script=join(SCRIPTS_DIR, "filter_ciriout.py"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     threads: getthreads("ciri")
     container: config['containers']['ciri']
     shell:
         """
-set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.outdir} {params.tmpdir}
 cd {params.outdir}
 if [ "{params.peorse}" == "PE" ];then
     ## paired-end
@@ -314,8 +302,8 @@ perl {params.ciripl} \\
 -F {params.reffa} \\
 -A {input.gtf} \\
 -G {output.cirilog} -T {threads}
-# samtools view -@{threads} -T {params.reffa} -CS {params.sample}.bwa.sam | samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O CRAM -o {output.ciribam} -
-samtools view -@{threads} -bS {params.sample}.bwa.sam | samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O BAM -o {output.ciribam} -
+# samtools view -@{threads} -T {params.reffa} -CS {params.sample}.bwa.sam | samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O CRAM -o {output.ciribam} -
+samtools view -@{threads} -bS {params.sample}.bwa.sam | samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.ciribam} -
 rm -rf {params.sample}.bwa.sam
 python {params.script} \\
     --ciriout {output.ciriout} \\
@@ -371,24 +359,19 @@ rule circExplorer_bwa:
         minsize_virus=config["minsize_virus"],
         maxsize_virus=config["maxsize_virus"],
         bash_script=join(SCRIPTS_DIR,"_run_circExplorer_bwa.sh"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
         # script=join(SCRIPTS_DIR, "circExplorer_get_annotated_counts_per_sample.py"),  # this produces an annotated counts table to which counts found in BAMs need to be appended
     threads: getthreads("circExplorer")
     container: config['containers']["circexplorer"]
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
-if [ ! -d {params.outdir} ];then mkdir {params.outdir};fi
+mkdir -p {params.tmpdir} {params.outdir}
+
 cd {params.outdir}
 bash {params.bash_script} \\
     --bwabam {input.ciribam} \\
-    --tmpdir $TMPDIR \\
+    --tmpdir {params.tmpdir} \\
     --outdir {params.outdir} \\
     --samplename {params.sample} \\
     --genepred {params.genepred} \\
@@ -690,7 +673,7 @@ rule dcc:
         dcc_strandedness=config["dcc_strandedness"],
         rep=REPEATS_GTF,
         fa=REF_FA,
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
         script=join(SCRIPTS_DIR, "create_dcc_per_sample_counts_table.py"),
         bsj_min_nreads=config["minreadcount"],
         refregions=REF_REGIONS,
@@ -705,17 +688,12 @@ rule dcc:
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.tmpdir}
 
 cd $(dirname {output.cr})
 if [ "{params.peorse}" == "PE" ];then
 DCC @{input.ss} \\
-    --temp ${{TMPDIR}}/DCC \\
+    --temp {params.tmpdir}/DCC \\
     --threads {threads} \\
     --detect --gene \\
     --bam {input.bam} \\
@@ -729,7 +707,7 @@ DCC @{input.ss} \\
     -mt2 @{input.m2}
 else
 DCC @{input.ss} \\
-    --temp ${{TMPDIR}}/DCC \\
+    --temp {params.tmpdir}/DCC \\
     --threads {threads} \\
     --detect --gene \\
     --bam {input.bam} \\
@@ -740,12 +718,12 @@ DCC @{input.ss} \\
     --refseq {params.fa} 
 fi
 
-ls -alrth ${{TMPDIR}}
+ls -alrth {params.tmpdir}
 
-paste {output.cr} {output.linear} | cut -f1-5,9 > ${{TMPDIR}}/CircRNALinearCount
+paste {output.cr} {output.linear} | cut -f1-5,9 > {params.tmpdir}/CircRNALinearCount
 
 python {params.script} \\
-  --CircCoordinates {output.cc} --CircRNALinearCount ${{TMPDIR}}/CircRNALinearCount -o {output.ct}
+  --CircCoordinates {output.cc} --CircRNALinearCount {params.tmpdir}/CircRNALinearCount -o {output.ct}
 
 python {params.script2} \\
     --in_dcc_counts_table {output.ct} \\
@@ -846,18 +824,13 @@ rule mapsplice:
         separate_fastas=join(REF_DIR, "separate_fastas"),
         ebwt=join(REF_DIR, "separate_fastas_index"),
         outdir=join(WORKDIR, "results", "{sample}", "MapSplice"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     threads: getthreads("mapsplice")
     container: config['containers']['mapsplice']
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.tmpdir}
 
 MSHOME="/opt/MapSplice2"
 # singularity exec -B /data/Ziegelbauer_lab,/data/kopardevn \
@@ -867,12 +840,12 @@ if [ "{params.peorse}" == "PE" ];then
 
 R1fn=$(basename {input.R1})
 R2fn=$(basename {input.R2})
-zcat {input.R1} > ${{TMPDIR}}/${{R1fn%.*}}
-zcat {input.R2} > ${{TMPDIR}}/${{R2fn%.*}}
+zcat {input.R1} > {params.tmpdir}/${{R1fn%.*}}
+zcat {input.R2} > {params.tmpdir}/${{R2fn%.*}}
 
 python $MSHOME/mapsplice.py \\
- -1 ${{TMPDIR}}/${{R1fn%.*}} \\
- -2 ${{TMPDIR}}/${{R2fn%.*}} \\
+ -1 {params.tmpdir}/${{R1fn%.*}} \\
+ -2 {params.tmpdir}/${{R2fn%.*}} \\
  -c {params.separate_fastas} \\
  -p {threads} \\
  --min-map-len {params.minmaplen} \\
@@ -887,10 +860,10 @@ python $MSHOME/mapsplice.py \\
 else
 
 R1fn=$(basename {input.R1})
-zcat {input.R1} > ${{TMPDIR}}/${{R1fn%.*}}
+zcat {input.R1} > {params.tmpdir}/${{R1fn%.*}}
 
 python $MSHOME/mapsplice.py \
- -1 ${{TMPDIR}}/${{R1fn%.*}} \
+ -1 {params.tmpdir}/${{R1fn%.*}} \
  -c {params.separate_fastas} \
  -p {threads} \
  -x {params.ebwt} \
@@ -945,7 +918,7 @@ rule mapsplice_postprocess:
     params:
         script=join(SCRIPTS_DIR, "create_mapsplice_per_sample_counts_table.py"),
         memG=getmemG("mapsplice_postprocess"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
         bsj_min_nreads=config["minreadcount"],
         refregions=REF_REGIONS,
         reffa=REF_FA,
@@ -960,12 +933,7 @@ rule mapsplice_postprocess:
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.tmpdir}
 python {params.script} \\
     --circularRNAstxt {input.circRNAs} \\
     -o {output.ct} \\
@@ -979,8 +947,8 @@ python {params.script} \\
     --host_filter_max {params.maxsize_host} \\
     --virus_filter_min {params.minsize_virus} \\
     --virus_filter_max {params.maxsize_virus}
-cd $TMPDIR
-samtools view -@{threads} -T {params.reffa} -CS {input.sam} | samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O CRAM -o alignments.cram -
+cd {params.tmpdir}
+samtools view -@{threads} -T {params.reffa} -CS {input.sam} | samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O CRAM -o alignments.cram -
 rsync -az --progress alignments.cram {output.bam}
 rsync -az --progress alignments.cram.crai {output.bai}
 """
@@ -1039,7 +1007,7 @@ rule nclscan:
         peorse=get_peorse,
         nclscan_config=config["nclscan_config"],
         script=join(SCRIPTS_DIR, "create_nclscan_per_sample_counts_table.py"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
         bsj_min_nreads=config["minreadcount"],
         refregions=REF_REGIONS,
         host=HOST,
@@ -1052,18 +1020,13 @@ rule nclscan:
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.tmpdir}
 outdir=$(dirname {output.result})
 results_bn=$(basename {output.result})
 
 if [ "{params.peorse}" == "PE" ];then
-NCLscan.py -c {params.nclscan_config} -pj {params.sample} -o $TMPDIR --fq1 {input.R1} --fq2 {input.R2}
-rsync -az --progress ${{TMPDIR}}/${{results_bn}} {output.result}
+NCLscan.py -c {params.nclscan_config} -pj {params.sample} -o {params.tmpdir} --fq1 {input.R1} --fq2 {input.R2}
+rsync -az --progress {params.tmpdir}/${{results_bn}} {output.result}
 python {params.script} \\
     --result {output.result} \\
     -o {output.ct} \\
@@ -1124,17 +1087,12 @@ rule circrnafinder:
         ),
     params:
         bsj_min_nreads=config["minreadcount"],
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']['circRNA_finder']
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.tmpdir}
 
 starDir=$(dirname {input.chimericsam})
 outDir=$(dirname {output.bed})
@@ -1199,7 +1157,7 @@ rule find_circ:
         find_circ_params=config['findcirc_params'],
         min_reads=config['circexplorer_bsj_circRNA_min_reads'],
         collapse_script=join(SCRIPTS_DIR,"_collapse_find_circ.py"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("find_circ")
     shell:
@@ -1207,14 +1165,8 @@ rule find_circ:
 set -exo pipefail
 python --version
 which python
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-
-if [ ! -d $TMPDIR ]; then mkdir -p $TMPDIR;fi
-cd $TMPDIR
+mkdir -p {params.tmpdir}
+cd {params.tmpdir}
 
 refdir=$(dirname {input.bt2})
 outdir=$(dirname {output.find_circ_bsj_bed})
@@ -1232,41 +1184,41 @@ outdir=$(dirname {output.find_circ_bsj_bed})
 # These _A and _B pairs should be retained in the fastq splits
 
 # find number of lines in fastq file
-cp {input.anchorsfq} ${{TMPDIR}}
+cp {input.anchorsfq} {params.tmpdir}
 fname=$(basename {input.anchorsfq})
 fname_wo_gz=$(echo $fname|sed "s/.gz//g")
 pigz -d $fname
 total_lines=$(wc -l ${{fname_wo_gz}} | awk '{{print $1}}')
 split_nlines=$(echo $total_lines| awk '{{print sprintf("%d", $1/10)}}' | awk '{{print sprintf("%d",($1+7)/8+1)}}' | awk '{{print sprintf("%d",$1*8)}}')
-split -d -l $split_nlines --suffix-length 1 $fname_wo_gz ${{TMPDIR}}/{params.sample}.samsplit.
+split -d -l $split_nlines --suffix-length 1 $fname_wo_gz {params.tmpdir}/{params.sample}.samsplit.
 
-if [ -f ${{TMPDIR}}/do_find_circ ];then rm -f ${{TMPDIR}}/do_find_circ;fi
+if [ -f {params.tmpdir}/do_find_circ ];then rm -f {params.tmpdir}/do_find_circ;fi
 
 for i in $(seq 0 9);do
     bowtie2 -p {threads} \\
         --score-min=C,-15.0 \\
         --reorder --mm \\
-        -q -U ${{TMPDIR}}/{params.sample}.samsplit.${{i}} \\
-        -x ${{refdir}}/ref > ${{TMPDIR}}/{params.sample}.samsplit.${{i}}.sam
+        -q -U {params.tmpdir}/{params.sample}.samsplit.${{i}} \\
+        -x ${{refdir}}/ref > {params.tmpdir}/{params.sample}.samsplit.${{i}}.sam
 
-cat <<EOF >>${{TMPDIR}}/do_find_circ
-cat ${{TMPDIR}}/{params.sample}.samsplit.${{i}}.sam | \\
+cat <<EOF >>{params.tmpdir}/do_find_circ
+cat {params.tmpdir}/{params.sample}.samsplit.${{i}}.sam | \\
 find_circ.py \\
     --genome={params.reffa} \\
     --prefix={params.sample}.find_circ \\
     --name={params.sample} \\
     {params.find_circ_params} \\
     --stats=${{outdir}}/{params.sample}.bowtie2_stats.${{i}}.txt \\
-    --reads=${{TMPDIR}}/{params.sample}.bowtie2_spliced_reads.${{i}}.fa \\
-    > ${{TMPDIR}}/{params.sample}.splice_sites.${{i}}.bed
+    --reads={params.tmpdir}/{params.sample}.bowtie2_spliced_reads.${{i}}.fa \\
+    > {params.tmpdir}/{params.sample}.splice_sites.${{i}}.bed
 EOF
 done
 
-parallel -j 10 < ${{TMPDIR}}/do_find_circ
+parallel -j 10 < {params.tmpdir}/do_find_circ
 
-cat ${{TMPDIR}}/{params.sample}.splice_sites.*.bed > ${{TMPDIR}}/{params.sample}.splice_sites.bed
+cat {params.tmpdir}/{params.sample}.splice_sites.*.bed > {params.tmpdir}/{params.sample}.splice_sites.bed
 
-grep CIRCULAR ${{TMPDIR}}/{params.sample}.splice_sites.bed | \\
+grep CIRCULAR {params.tmpdir}/{params.sample}.splice_sites.bed | \\
     grep ANCHOR_UNIQUE \\
     > {output.find_circ_bsj_bed}
 
diff --git a/workflow/rules/init.smk b/workflow/rules/init.smk
index 8429588..9aea06c 100644
--- a/workflow/rules/init.smk
+++ b/workflow/rules/init.smk
@@ -86,6 +86,10 @@ def _convert_to_int(variable):
 
 # resource absolute path
 WORKDIR = config["workdir"]
+TEMPDIR = config["tempdir"]
+if not os.access(TEMPDIR, os.W_OK):
+    raise PermissionError(f"TEMPDIR {TEMPDIR} cannot be written to.\n\tHint: does the path exist and do you have write permissions?")
+
 SCRIPTS_DIR = config["scriptsdir"]
 RESOURCES_DIR = config["resourcesdir"]
 FASTAS_GTFS_DIR = config["fastas_gtfs_dir"]
@@ -106,6 +110,7 @@ MAPSPLICE_FILTERING = config["mapsplice_filtering"]
 FLANKSIZE = config['flanksize']
 HQCC=config["high_confidence_core_callers"].replace(" ","")
 CALLERS=["circExplorer","ciri","circExplorer_bwa"]
+
 # if RUN_CLEAR: CALLERS.append("clear")
 if RUN_DCC: CALLERS.append("dcc")
 if RUN_MAPSPLICE: CALLERS.append("mapsplice")
diff --git a/workflow/rules/post_findcircrna_processing.smk b/workflow/rules/post_findcircrna_processing.smk
index 7eeebb0..8368811 100644
--- a/workflow/rules/post_findcircrna_processing.smk
+++ b/workflow/rules/post_findcircrna_processing.smk
@@ -61,18 +61,13 @@ rule create_circExplorer_BSJ_bam:
         scriptse=join(SCRIPTS_DIR, "_create_circExplorer_BSJ_bam_se.py"),
         flankscript=join(SCRIPTS_DIR, "_append_splice_site_flanks_to_BSJs.py"),
         bam2bwscript=join(SCRIPTS_DIR, "bam_to_bigwig.sh"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']["star_ucsc_cufflinks"]
     threads: getthreads("create_circExplorer_BSJ_bam")
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
+mkdir -p {params.tmpdir}
 
 outdir=$(dirname {output.BSJbam})
 BSJbedbn=$(basename {output.BSJbed})
@@ -82,59 +77,59 @@ if [ "{params.peorse}" == "PE" ];then
 python3 {params.scriptpe} \\
     --inbam {input.chimericbam} \\
     --sample_counts_table {input.countstable} \\
-    --plusbam ${{TMPDIR}}/{params.sample}.BSJ.plus.bam \\
-    --minusbam ${{TMPDIR}}/{params.sample}.BSJ.minus.bam \\
-    --outbam ${{TMPDIR}}/{params.sample}.BSJ.bam \\
-    --bed ${{TMPDIR}}/${{BSJbedbn}} \\
+    --plusbam {params.tmpdir}/{params.sample}.BSJ.plus.bam \\
+    --minusbam {params.tmpdir}/{params.sample}.BSJ.minus.bam \\
+    --outbam {params.tmpdir}/{params.sample}.BSJ.bam \\
+    --bed {params.tmpdir}/${{BSJbedbn}} \\
     --sample_name {params.sample} \\
     --junctionsfound {output.BSJfoundcounts} \\
     --regions {params.refregions} \\
     --host "{params.host}" \\
     --additives "{params.additives}" \\
     --viruses "{params.viruses}" \\
-    --outputhostbams --outputvirusbams --outdir $TMPDIR
+    --outputhostbams --outputvirusbams --outdir {params.tmpdir}
 
 else
 
 python3 {params.scriptse} \\
     --inbam {input.chimericbam} \\
     --sample_counts_table {input.countstable} \\
-    --plusbam ${{TMPDIR}}/{params.sample}.BSJ.plus.bam \\
-    --minusbam ${{TMPDIR}}/{params.sample}.BSJ.minus.bam \\
-    --outbam ${{TMPDIR}}/{params.sample}.BSJ.bam \\
-    --bed ${{TMPDIR}}/${{BSJbedbn}} \\
+    --plusbam {params.tmpdir}/{params.sample}.BSJ.plus.bam \\
+    --minusbam {params.tmpdir}/{params.sample}.BSJ.minus.bam \\
+    --outbam {params.tmpdir}/{params.sample}.BSJ.bam \\
+    --bed {params.tmpdir}/${{BSJbedbn}} \\
     --sample_name {params.sample} \\
     --junctionsfound {output.BSJfoundcounts} \\
     --regions {params.refregions} \\
     --host "{params.host}" \\
     --additives "{params.additives}" \\
     --viruses "{params.viruses}" \\
-    --outputhostbams --outputvirusbams --outdir $TMPDIR
+    --outputhostbams --outputvirusbams --outdir {params.tmpdir}
 
 fi
 
-samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O BAM -o {output.plusBSJbam} ${{TMPDIR}}/{params.sample}.BSJ.plus.bam 
-samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O BAM -o {output.minusBSJbam} ${{TMPDIR}}/{params.sample}.BSJ.minus.bam 
-samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O BAM -o {output.BSJbam} ${{TMPDIR}}/{params.sample}.BSJ.bam
+samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.plusBSJbam} {params.tmpdir}/{params.sample}.BSJ.plus.bam 
+samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.minusBSJbam} {params.tmpdir}/{params.sample}.BSJ.minus.bam 
+samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.BSJbam} {params.tmpdir}/{params.sample}.BSJ.bam
 
 for b in {output.plusBSJbam} {output.minusBSJbam} {output.BSJbam} 
 # for b in {output.plusBSJbam} {output.minusBSJbam}
 do
-    bash {params.bam2bwscript} $b $TMPDIR
+    bash {params.bam2bwscript} $b {params.tmpdir}
 done
 
 for i in $(echo {params.host}|tr ',' ' ');do 
-    samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O BAM -o ${{outdir}}/{params.sample}.${{i}}.BSJ.bam ${{TMPDIR}}/{params.sample}.${{i}}.BSJ.bam
-    bash {params.bam2bwscript} ${{outdir}}/{params.sample}.${{i}}.BSJ.bam $TMPDIR
+    samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}/{params.sample}.${{i}}.BSJ.bam
+    bash {params.bam2bwscript} ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}
 done
 for i in $(echo {params.viruses}|tr ',' ' ');do 
-    samtools sort -l 9 -T $TMPDIR --write-index -@{threads} -O BAM -o ${{outdir}}/{params.sample}.${{i}}.BSJ.bam ${{TMPDIR}}/{params.sample}.${{i}}.BSJ.bam
-    bash {params.bam2bwscript} ${{outdir}}/{params.sample}.${{i}}.BSJ.bam $TMPDIR
+    samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}/{params.sample}.${{i}}.BSJ.bam
+    bash {params.bam2bwscript} ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}
 done
 
-python3 {params.flankscript} --reffa {params.reffa} --inbsjbedgz ${{TMPDIR}}/${{BSJbedbn}} --outbsjbedgz {output.BSJbed}
+python3 {params.flankscript} --reffa {params.reffa} --inbsjbedgz {params.tmpdir}/${{BSJbedbn}} --outbsjbedgz {output.BSJbed}
 
-rm -rf $TMPDIR
+rm -rf {params.tmpdir}
 """
 
 
@@ -209,19 +204,14 @@ rule create_circExplorer_linear_spliced_bams:
         peorse=get_peorse,
         bashscript=join(SCRIPTS_DIR, "_create_circExplorer_linear_bam.v2.sh"),
         outdir=join(WORKDIR, "results", "{sample}", "circExplorer"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']["star_ucsc_cufflinks"]
     threads: getthreads("create_circExplorer_linear_spliced_bams")
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-fi
-if [ -d $TMPDIR ];then rm -rf $TMPDIR;fi
-mkdir -p $TMPDIR
+if [ -d {params.tmpdir} ];then rm -rf {params.tmpdir};fi
+mkdir -p {params.tmpdir}
 
 cd {params.outdir}
 
@@ -232,7 +222,7 @@ bash {params.bashscript} \\
     --samplename {params.sample} \\
     --peorse {params.peorse} \\
     --bsjbed {input.bsjbedgz} \\
-    --tmpdir $TMPDIR \\
+    --tmpdir {params.tmpdir} \\
     --rid2jid {output.rid2jid} \\
     --filteredbam {output.filtered_bam} \\
     --linearbsjlist {output.linear_readids} \\
@@ -247,7 +237,7 @@ bash {params.bashscript} \\
     --linearbam {output.linear_bam} \\
     --splicedbam {output.spliced_bam} \\
     --threads {threads}
-rm -rf $TMPDIR
+rm -rf {params.tmpdir}
 """
 
 
@@ -290,16 +280,11 @@ rule create_circExplorer_merged_found_counts_table:
             SCRIPTS_DIR, "create_circExplorer_per_sample_counts_table.py"
         ),
         outdir=join(WORKDIR, "results", "{sample}", "circExplorer"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     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
+mkdir -p {params.tmpdir}
 python3 {params.pythonscript} \\
     -b {input.bsj_found_counts} \\
     -l {input.linear_spliced_counts} \\
@@ -312,32 +297,6 @@ python3 {params.pythonscript2} \\
 """
 
 
-# localrules: create_circExplorer_per_sample_counts_table
-# rule create_circExplorer_per_sample_counts_table:
-#     input:
-#         annotation_counts=rules.circExplorer.output.annotation_counts_table,
-#         found_counts=rules.create_circExplorer_merged_found_counts_table.output.found_counts_table
-#     output:
-#         count_counts_table=join(WORKDIR,"results","{sample}","circExplorer","{sample}.circExplorer.counts_table.tsv")
-#     params:
-#         sample="{sample}",
-#         pythonscript=join(SCRIPTS_DIR,"create_circExplorer_per_sample_counts_table.py"),
-#         outdir=join(WORKDIR,"results","{sample}","circExplorer"),
-#         randomstr=str(uuid.uuid4())
-#     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
-# python3 {params.pythonscript} \\
-#     --annotationcounts {input.annotation_counts} \\
-#     --allfoundcounts {input.found_counts} \\
-#     --countstable {output.count_counts_table}
-# """
-
 if RUN_MAPSPLICE:
 
     rule alignment_stats:
@@ -357,32 +316,27 @@ if RUN_MAPSPLICE:
             peorse=get_peorse,
             run_mapsplice=N_RUN_MAPSPLICE,
             bash2nreads_pyscript=join(SCRIPTS_DIR, "_bam_get_alignment_stats.py"),
-            randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
         threads: getthreads("alignment_stats")
         container: config['containers']["base"]
         shell:
             """
     set -exo pipefail
-    if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-        TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-    else
-        TMPDIR="/dev/shm/{params.randomstr}"
-        mkdir -p $TMPDIR
-    fi
+    mkdir -p {params.tmpdir}
     for bamfile in {input};do
         bamfile_bn=$(basename $bamfile)
         if [ "{params.peorse}" == "PE" ];then
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > ${{TMPDIR}}/${{bamfile_bn}}.counts"
+        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > {params.tmpdir}/${{bamfile_bn}}.counts"
         else
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > ${{TMPDIR}}/${{bamfile_bn}}.counts"
+        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > {params.tmpdir}/${{bamfile_bn}}.counts"
         fi
-    done > ${{TMPDIR}}/do_bamstats
-    parallel -j 2 < ${{TMPDIR}}/do_bamstats
+    done > {params.tmpdir}/do_bamstats
+    parallel -j 2 < {params.tmpdir}/do_bamstats
 
     print_bam_results () {{
         bamfile=$1
         bamfile_bn=$(basename $bamfile)
-        stats_file=${{TMPDIR}}/${{bamfile_bn}}.counts
+        stats_file={params.tmpdir}/${{bamfile_bn}}.counts
         prefix=$2
         while read b a;do echo -ne "${{prefix}}_${{a}}\\t${{b}}\\n";done < $stats_file
     }}
@@ -412,32 +366,27 @@ else:
             peorse=get_peorse,
             run_mapsplice=N_RUN_MAPSPLICE,
             bash2nreads_pyscript=join(SCRIPTS_DIR, "_bam_get_alignment_stats.py"),
-            randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
         threads: getthreads("alignment_stats")
         container: config['containers']["base"]
         shell:
             """
     set -exo pipefail
-    if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-        TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-    else
-        TMPDIR="/dev/shm/{params.randomstr}"
-        mkdir -p $TMPDIR
-    fi
+    mkdir -p {params.tmpdir}
     for bamfile in {input};do
         bamfile_bn=$(basename $bamfile)
         if [ "{params.peorse}" == "PE" ];then
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > ${{TMPDIR}}/${{bamfile_bn}}.counts"
+        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > {params.tmpdir}/${{bamfile_bn}}.counts"
         else
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > ${{TMPDIR}}/${{bamfile_bn}}.counts"
+        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > {params.tmpdir}/${{bamfile_bn}}.counts"
         fi
-    done > ${{TMPDIR}}/do_bamstats
-    parallel -j 2 < ${{TMPDIR}}/do_bamstats
+    done > {params.tmpdir}/do_bamstats
+    parallel -j 2 < {params.tmpdir}/do_bamstats
 
     print_bam_results () {{
         bamfile=$1
         bamfile_bn=$(basename $bamfile)
-        stats_file=${{TMPDIR}}/${{bamfile_bn}}.counts
+        stats_file={params.tmpdir}/${{bamfile_bn}}.counts
         prefix=$2
         while read b a;do echo -ne "${{prefix}}_${{a}}\\t${{b}}\\n";done < $stats_file
     }}
@@ -467,25 +416,21 @@ rule merge_alignment_stats:
     output:
         join(WORKDIR, "results", "alignmentstats.txt"),
     params:
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     shell:
         """
 set -exo pipefail
-if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-    TMPDIR="/lscratch/${{SLURM_JOB_ID}}"
-else
-    TMPDIR="/dev/shm/{params.randomstr}"
-    mkdir -p $TMPDIR
-fi
+mkdir -p {params.tmpdir}
+
 count=0
 for f in {input};do
     count=$((count+1))
     if [ "$count" == "1" ];then
         cp $f {output}
     else
-        cut -f2 $f > ${{TMPDIR}}/${{count}}
-        paste {output} ${{TMPDIR}}/${{count}} > ${{TMPDIR}}/${{count}}.tmp
-        mv ${{TMPDIR}}/${{count}}.tmp {output}
+        cut -f2 $f > {params.tmpdir}/${{count}}
+        paste {output} {params.tmpdir}/${{count}} > {params.tmpdir}/${{count}}.tmp
+        mv {params.tmpdir}/${{count}}.tmp {output}
     fi
 done 
 """
diff --git a/workflow/rules/preprocessing.smk b/workflow/rules/preprocessing.smk
index e3a83f7..1abeaed 100644
--- a/workflow/rules/preprocessing.smk
+++ b/workflow/rules/preprocessing.smk
@@ -30,23 +30,14 @@ rule cutadapt:
         cutadapt_O=config["cutadapt_O"],
         cutadapt_q=config["cutadapt_q"],
         adapters=join(RESOURCES_DIR, "TruSeq_and_nextera_adapters.consolidated.fa"),
-        randomstr=str(uuid.uuid4()),
+        tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
     container: config['containers']['cutadapt']
     threads: getthreads("cutadapt")
     shell:
         """
         set -exo pipefail
 
-        # set TMPDIR
-        if [ -d /lscratch/${{SLURM_JOB_ID}} ];then
-            TMPDIR="/lscratch/${{SLURM_JOB_ID}}/{params.randomstr}"
-        else
-            TMPDIR="/dev/shm/{params.randomstr}"
-        fi
-        if [ ! -d $TMPDIR ];then mkdir -p $TMPDIR;fi
-
-        if [ ! -d {params.outdir} ];then mkdir {params.outdir};fi
-
+        mkdir -p {params.tmpdir}
         of1bn=$(basename {output.of1})
         of2bn=$(basename {output.of2})
 
@@ -61,14 +52,14 @@ rule cutadapt:
             -b file:{params.adapters} \\
             -B file:{params.adapters} \\
             -j {threads} \\
-            -o ${{TMPDIR}}/${{of1bn}} -p ${{TMPDIR}}/${{of2bn}} \\
+            -o {params.tmpdir}/${{of1bn}} -p {params.tmpdir}/${{of2bn}} \\
             {input.R1} {input.R2}
             
         # filter for average read quality
             fastq-filter \\
                 -q {params.cutadapt_q} \\
                 -o {output.of1} -o {output.of2} \\
-                ${{TMPDIR}}/${{of1bn}} ${{TMPDIR}}/${{of2bn}}
+                {params.tmpdir}/${{of1bn}} {params.tmpdir}/${{of2bn}}
 
         else
             ## Single-end
@@ -80,7 +71,7 @@ rule cutadapt:
             -q {params.cutadapt_q},{params.cutadapt_q} -m {params.cutadapt_min_length} \\
             -b file:{params.adapters} \\
             -j {threads} \\
-            -o ${{TMPDIR}}/${{of1bn}} \\
+            -o {params.tmpdir}/${{of1bn}} \\
             {input.R1}
             
             touch {output.of2}
@@ -89,7 +80,7 @@ rule cutadapt:
             fastq-filter \\
                 -q {params.cutadapt_q} \\
                 -o {output.of1} \\
-                ${{TMPDIR}}/${{of1bn}}
+                {params.tmpdir}/${{of1bn}}
 
         fi
         """