diff --git a/envs/dummy_env.yaml b/envs/dummy_env.yaml
deleted file mode 100644
index e69de29..0000000
diff --git a/rules/align.smk b/rules/align.smk
deleted file mode 100644
index 70e09e1..0000000
--- a/rules/align.smk
+++ /dev/null
@@ -1,90 +0,0 @@
-# if config['bsjfa']:
-#     BSJFA=config['bsjfa']
-# else:
-#     BSJFA=config['bsjfadefault']
-# check_readaccess(BSJFA)
-PRIMERINFO=config['primertsv']
-check_readaccess(PRIMERINFO)
-REFFA=config['reffa']
-check_readaccess(REFFA)
-
-rule create_primerbed:
-    input:
-        primertsv=PRIMERINFO
-    output:
-        primerbed=join(WORKDIR,"bowtie_index","primers.bed")
-    params:
-        script=join(SCRIPTSDIR,"build_primer_bed.py")
-    envmodules: TOOLS["python37"]["version"]
-    shell:"""
-python {params.script} {input.primertsv} > {output.primerbed}
-"""
-
-rule create_bsjfa:
-    input:
-        bed=rules.create_primerbed.output.primerbed,
-        reffa=REFFA
-    output:
-        bsjfa=join(WORKDIR,"bowtie_index","bsj.fa")
-    params:
-        script=join(SCRIPTSDIR,"generate_bsj_fasta_from_primer_bed.py")
-    container: "docker://nciccbr/ccbr_htseq_0.13.5:latest"
-    shell:"""
-python {params.script} \
---bed {input.bed} \
---reffa {input.reffa} \
---outfa {output.bsjfa}
-"""
-
-rule build_index:
-    input:
-        bsjfa=rules.create_bsjfa.output.bsjfa,
-    output:
-        join(WORKDIR,"bowtie_index","bsj.1.bt2")
-    params:
-        outdir=join(WORKDIR,"bowtie_index")
-    envmodules: TOOLS["bowtie2"]["version"]
-    threads: 2
-    shell: """
-# cp {input.bsjfa} {params.outdir}
-cd {params.outdir}
-bsjfa=$(basename {input.bsjfa})
-bowtie2-build $bsjfa bsj
-# gzip -n -f {input.bsjfa}
-"""
-
-rule align:
-    input:
-        r1=rules.cutadapt.output.of1,
-        r2=rules.cutadapt.output.of2,
-        bt2_index=rules.build_index.output,
-    output:
-        bam=join(WORKDIR,"results","{sample}","bam","{sample}.bam")
-    params:
-        sample="{sample}",
-        workdir=WORKDIR,
-        outdir=join(WORKDIR,"results","{sample}","bowtie2"),
-        peorse=get_peorse,
-        bowtie2_alignment_parameters=config["bowtie2_alignment_parameters"],
-        mem=MEMORY
-    threads: 56
-    envmodules: TOOLS["bowtie2"]["version"], TOOLS["sambamba"]["version"]
-    shell:"""
-bt2_index=$(echo "{input.bt2_index}"|awk -F".1.bt2" '{{print $1}}')
-if [ "{params.peorse}" == "PE" ];then
-    bowtie2 \
-    --threads {threads} \
-    {params.bowtie2_alignment_parameters} \
-    -x $bt2_index \
-    -U {input.r1},{input.r2}
-else
-    bowtie2 \
-    --threads {threads} \
-    {params.bowtie2_alignment_parameters} \
-    -x $bt2_index \
-    -U {input.r1}
-fi \
-| awk -F"\\t" '{{if ($6 ~ /60M/ || $1 ~ /^@/){{print}}}}' \
-| sambamba view --nthreads={threads} -S --format=bam -o=/dev/stdout /dev/stdin \
-| sambamba sort --memory-limit={params.mem}G --tmpdir=/dev/shm --nthreads={threads} --out={output.bam} /dev/stdin
-"""
diff --git a/rules/init.smk b/rules/init.smk
deleted file mode 100644
index fb87a25..0000000
--- a/rules/init.smk
+++ /dev/null
@@ -1,96 +0,0 @@
-import shutil
-import sys
-import os
-import pandas as pd
-import yaml
-import glob
-
-CONFIGFILE = str(workflow.overwrite_configfiles[0])
-
-def check_existence(filename):
-	"""Checks if file exists on filesystem
-	:param filename <str>: Name of file to check
-	"""
-	filename=filename.strip()
-	if not os.path.exists(filename):
-		sys.exit("File: {} does not exists!".format(filename))
-	return True
-
-
-def check_readaccess(filename):
-	"""Checks permissions to see if user can read a file
-	:param filename <str>: Name of file to check
-	"""
-	filename=filename.strip()
-	check_existence(filename)
-	if not os.access(filename,os.R_OK):
-		sys.exit("File: {} exists, but user cannot read from file due to permissions!".format(filename))
-	return True
-
-
-def check_writeaccess(filename):
-	"""Checks permissions to see if user can write to a file
-	:param filename <str>: Name of file to check
-	"""
-	filename=filename.strip()
-	check_existence(filename)
-	if not os.access(filename,os.W_OK):
-		sys.exit("File: {} exists, but user cannot write to file due to permissions!".format(filename))
-	return True
-
-
-#
-MEMORY="100"
-# get working dir from config
-WORKDIR = config["workdir"]
-
-# get resources folder
-try:
-	RESOURCESDIR = config["resourcesdir"]
-except KeyError:
-	RESOURCESDIR = join(WORKDIR,"resources")
-
-# get scripts folder
-try:
-	SCRIPTSDIR = config["scriptsdir"]
-except KeyError:
-	SCRIPTSDIR = join(WORKDIR,"scripts")
-
-## Load tools from YAML file
-with open(config["tools"]) as f:
-	TOOLS = yaml.safe_load(f)
-
-if not os.path.exists(join(WORKDIR,"fastqs")):
-	os.mkdir(join(WORKDIR,"fastqs"))
-if not os.path.exists(join(WORKDIR,"results")):
-	os.mkdir(join(WORKDIR,"results"))
-for f in ["samples", "tools", "cluster"]:
-	check_readaccess(config[f])
-
-SAMPLESDF = pd.read_csv(config["samples"],sep="\t",header=0,index_col="sampleName")
-SAMPLES = list(SAMPLESDF.index)
-SAMPLESDF["R1"]=join(RESOURCESDIR,"dummy")
-SAMPLESDF["R2"]=join(RESOURCESDIR,"dummy")
-SAMPLESDF["PEorSE"]="PE"
-
-for sample in SAMPLES:
-	R1file=SAMPLESDF["path_to_R1_fastq"][sample]
-	R2file=SAMPLESDF["path_to_R2_fastq"][sample]
-	# print(sample,R1file,R2file)
-	check_readaccess(R1file)
-	R1filenewname=join(WORKDIR,"fastqs",sample+".R1.fastq.gz")
-	if not os.path.exists(R1filenewname):
-		os.symlink(R1file,R1filenewname)
-	SAMPLESDF.loc[[sample],"R1"]=R1filenewname
-	if str(R2file)!='nan':
-		check_readaccess(R2file)
-		R2filenewname=join(WORKDIR,"fastqs",sample+".R2.fastq.gz")
-		if not os.path.exists(R2filenewname):
-			os.symlink(R2file,R2filenewname)
-		SAMPLESDF.loc[[sample],"R2"]=R2filenewname
-	else:
-		SAMPLESDF.loc[[sample],"PEorSE"]="SE"
-# print(SAMPLESDF)
-# sys.exit()
-
-
diff --git a/rules/quant.smk b/rules/quant.smk
deleted file mode 100644
index 6637037..0000000
--- a/rules/quant.smk
+++ /dev/null
@@ -1,49 +0,0 @@
-BSJFA=rules.create_bsjfa.output.bsjfa
-
-rule salmon:
-    input:
-        bam=rules.align.output.bam,
-        reffa=BSJFA,
-    output:
-        sf=join(WORKDIR,"results","{sample}","salmon","quant.sf")
-    params:
-        salmon_parameters=config["salmon_parameters"]
-    envmodules: TOOLS["salmon"]["version"]
-    shell:"""
-outdir=$(dirname {output.sf})
-salmon quant \
---threads {threads} \
-{params.salmon_parameters} \
--t {input.reffa} \
--a {input.bam} \
---output $outdir
-"""
-
-rule aggregate_quant:
-    input:
-        expand(join(WORKDIR,"results","{sample}","salmon","quant.sf"),sample=SAMPLES)
-    output:
-        mergedquant=join(WORKDIR,"results","mergedquant.tsv"),
-        filteredmergedquant=join(WORKDIR,"results","mergedquant.filtered.tsv")
-    params:
-        rowsumfilter=config['aggregate_quant_rowsum_filter']
-    envmodules: TOOLS["salmon"]["version"]
-    shell:"""
-names=""
-quants=""
-for i in {input};do
-    outdir=$(dirname $i)
-    quants="$quants $outdir"
-    samplename=$(echo $outdir|awk -F"/" '{{print $(NF-1)}}')
-    names="$names $samplename"
-done
-salmon quantmerge --quants $quants --names $names --column numreads -o {output.mergedquant}
-head -n1 {output.mergedquant} > {output.filteredmergedquant}
-tail -n +2 {output.mergedquant} |\
-awk -F"\\t" -v r={params.rowsumfilter} -v OFS="\\t" '{{for(i=2;i<=NF;i++){{sum[NR]=sum[NR]+$i}};if (sum[NR] >= r) {{print sum[NR],$0}}}}' |\
-sort -k1,1gr |\
-cut -f2- >> {output.filteredmergedquant}
-"""
-
-
-    
\ No newline at end of file
diff --git a/rules/trim.smk b/rules/trim.smk
deleted file mode 100644
index 9fe2ff5..0000000
--- a/rules/trim.smk
+++ /dev/null
@@ -1,51 +0,0 @@
-def get_fastqs(wildcards):
-    d=dict()
-    d["R1"]=SAMPLESDF["R1"][wildcards.sample]
-    d["R2"]=SAMPLESDF["R2"][wildcards.sample]
-    return d
-
-def get_peorse(wildcards):
-    return SAMPLESDF["PEorSE"][wildcards.sample]
-
-rule cutadapt:
-    input:
-        unpack(get_fastqs)
-    output:
-        of1=join(WORKDIR,"results","{sample}","trim","{sample}.R1.trim.fastq.gz"),
-        of2=join(WORKDIR,"results","{sample}","trim","{sample}.R2.trim.fastq.gz")
-    params:
-        sample="{sample}",
-        workdir=WORKDIR,
-        outdir=join(WORKDIR,"results","{sample}"),
-        peorse=get_peorse,
-        adapters=join(RESOURCESDIR,"TruSeq_and_nextera_adapters.consolidated.fa")
-    envmodules: TOOLS["cutadapt"]["version"]
-    threads: 56
-    shell:"""
-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 35:35 \
-    -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 35 \
-    -b file:{params.adapters} \
-    -j {threads} \
-    -o {output.of1} \
-    {input.R1}
-    touch {output.of2}
-fi
-"""
\ No newline at end of file
diff --git a/scripts/build_primer_bed.py b/scripts/build_primer_bed.py
deleted file mode 100644
index c667c93..0000000
--- a/scripts/build_primer_bed.py
+++ /dev/null
@@ -1,32 +0,0 @@
-import sys
-primerstsv=open(sys.argv[1]).readlines()
-primerstsv.pop(0)
-primers=dict()
-for i in primerstsv:
-	i=i.strip().split("\t")
-	circRNAnamesplit=i[0].split("_")
-	circRNAname="_".join(circRNAnamesplit[:-1])
-	if not circRNAname in primers:
-		primers[circRNAname]=dict()
-		primers[circRNAname]["coordinates"]=list()
-	ForR=circRNAnamesplit[-1][0]
-	primers[circRNAname]["chrom"]=i[1]
-	strand=i[4]
-	primers[circRNAname]["coordinates"].append(int(i[2]))
-	primers[circRNAname]["coordinates"].append(int(i[3]))
-	primers[circRNAname]["coordinates"].sort()
-	if ForR == "F":
-		primers[circRNAname]["strand"]=strand
-	if ForR == "F" and strand == "+":
-		primers[circRNAname]["ASorSS"]="SS"
-	if ForR == "F" and strand == "-":
-		primers[circRNAname]["ASorSS"]="AS"
-for primer in primers:
-	sname=primer+"_"+primers[primer]["ASorSS"]
-	#sname="_".join([primer,primers[primer]["ASorSS"])
-	#print(sname)
-	chrom=primers[primer]["chrom"]
-	start=str(primers[primer]["coordinates"][0])
-	end=str(primers[primer]["coordinates"][-1])
-	strand=primers[primer]["strand"]
-	print("\t".join([chrom,start,end,sname,".",strand]))
diff --git a/scripts/gather_cluster_stats.sh b/scripts/gather_cluster_stats.sh
deleted file mode 100644
index 49c326e..0000000
--- a/scripts/gather_cluster_stats.sh
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/bin/bash
-## AUTHOR : Vishal N. Koparde, Ph.D., CCBR, NCI
-## DATE : Feb 2021
-## This scripts gathers cluster related statistics for jobs run on Biowulf using Snakemake by:
-##   > extracting "external" jobids from snakemake.log files
-##   > gather cluster stats for each job using "jobdata" and "jobhist" commands
-##   > sorts output by job submission time
-##   > output TSV file
-##
-
-function node2runpartition {
-	node=$1
-	partitions_requested=$2
-	run_partition=$(for p in `echo $partitions_requested|awk '{print $NF}'|tr "," " "`;do if [ "$(freen -N $node|grep $p|awk '{print $1}'|grep $p|wc -l)" == "1" ]; then echo $p;break 1;fi;done)
-	if [ "$run_partition" == "" ];then
-		echo "unknown"
-	else
-		echo "$run_partition"
-	fi
-}
-
-
-function get_jobid_stats {
-jobid=$1
-declare -A jobdataarray
-notaccountablejob=$(jobhist $jid|grep "No accounting"|wc -l)
-if [ "$notaccountablejob" == "1" ];then
-	jobdataarray["submit_time"]="JOBNOTACCOUNTABLE"
-	jobdataarray["jobid"]="$jobid"
-else
-	jobdata $jobid > ${jobid}.tmp
-	awk -F"\t" '{if (NF==2) {print}}' ${jobid}.tmp > ${jobid}.data && rm -f ${jobid}.tmp
-	while read a b;do
-		jobdataarray["$a"]="$b"
-	done < ${jobid}.data
-	rm -f ${jobid}.data
-	st=${jobdataarray["submit_time"]}
-	jobdataarray["human_submit_time"]=$(date -d @$st|sed "s/ /_/g")
-	jobdataarray["alloc_node_partition"]=$(node2runpartition ${jobdataarray["alloc_node"]} ${jobdataarray["partition"]})
-	jobdataarray["run_node_partition"]=$(node2runpartition ${jobdataarray["node_list"]} ${jobdataarray["partition"]})
-fi
-echo -ne "${jobdataarray["submit_time"]}\t"
-echo -ne "${jobdataarray["human_submit_time"]}\t"
-echo -ne "${jobdataarray["jobid"]}:${jobdataarray["state"]}:${jobdataarray["job_name"]}\t"
-echo -ne "${jobdataarray["alloc_node"]}:${jobdataarray["alloc_node_partition"]}:${jobdataarray["node_list"]}:${jobdataarray["run_node_partition"]}\t"
-echo -ne "${jobdataarray["queued"]}:${jobdataarray["elapsed"]}:${jobdataarray["time_limit"]}\t"
-echo -ne "${jobdataarray["avg_cpus"]}:${jobdataarray["max_cpu_used"]}:${jobdataarray["cpus_per_task"]}\t"
-echo -ne "${jobdataarray["avg_mem"]}:${jobdataarray["max_mem_used"]}:${jobdataarray["total_mem"]}\t"
-echo -ne "${jobdataarray["partition"]}:${jobdataarray["qos"]}\t"
-echo -ne "${jobdataarray["username"]}:${jobdataarray["groupname"]}:${jobdataarray["account"]}\t"
-echo -ne "${jobdataarray["work_dir"]}\t"
-echo -ne "${jobdataarray["std_out"]}\t"
-echo -ne "${jobdataarray["std_err"]}\n"
-}
-
-if [ "$#" != "1" ];then
-	echo " bash $0 <snakemake log file> "
-	exit 1
-fi
-
-snakemakelogfile=$1
-grep "with external jobid" $snakemakelogfile | awk '{print $NF}' | sed "s/['.]//g" | sort | uniq > ${snakemakelogfile}.jobids.lst
-echo -ne "##SubmitTime\tHumanSubmitTime\tJobID:JobState:JobName\tAllocNode:AllocNodePartition:RunNode:RunNodePartition\tQueueTime:RunTime:TimeLimit\tAvgCPU:MaxCPU:CPULimit\tAvgMEM:MaxMEM:MEMLimit\tPartition:QOS\tUsername:Group:Account\tWorkdir\tStdOut\tStdErr\n"
-while read jid;do
-	get_jobid_stats $jid
-done < ${snakemakelogfile}.jobids.lst |sort -k1,1n
-rm -f ${snakemakelogfile}.jobids.lst
\ No newline at end of file
diff --git a/scripts/generate_bsj_fasta_from_primer_bed.py b/scripts/generate_bsj_fasta_from_primer_bed.py
deleted file mode 100644
index b82f293..0000000
--- a/scripts/generate_bsj_fasta_from_primer_bed.py
+++ /dev/null
@@ -1,54 +0,0 @@
-import HTSeq
-import sys
-import argparse
-import os
-
-def read_bed_file(filename):
-	bedfile=open(filename,'r')
-	primers=dict()
-	for f in bedfile.readlines():
-		f=f.strip().split("\t")
-		primer=f[3]
-		primers[primer]=dict()
-		primers[primer]["chrom"]=f[0]
-		primers[primer]["start"]=int(f[1])
-		primers[primer]["end"]=int(f[2])
-		primers[primer]["strand"]=f[5]
-	return primers
-
-parser = argparse.ArgumentParser(description='Create fasta file from divergent primers bed file')
-parser.add_argument('--bed', dest='primerbed', type=str, required=True,
-                    help='Divergent primers bed file with min. 4 columns (chr,start,end,name)')
-parser.add_argument('--reffa', dest='reffa', type=str, required=True,
-                    help='reference fasta')
-parser.add_argument('--outfa', dest='outfa', type=str, required=True,
-                    help='output fasta')
-parser.add_argument('--scanlength', dest='scanlen', type=int, required=False, default=200,
-                    help='scan length...even positive number(default 200)')
-parser.add_argument('--flankmax', dest='flankmax', type=int, required=False, default=30,
-                    help='flankmax (default 30)')
-args = parser.parse_args()
-# sequences = dict( (s.name, s) for s in HTSeq.FastaReader(args.reffa) )
-sequences = dict( (s[1], s[0]) for s in HTSeq.FastaReader(args.reffa, raw_iterator=True) )
-# sequences = dict( (s[1], s[0]) for s in HTSeq.FastaReader(args.reffa) )
-primers = read_bed_file(args.primerbed)
-# print(primers)
-# for primer in primers:
-# 	print(primers[primer]["chrom"])
-outfastafile = open( args.outfa, "w" )
-offset = "N"*300
-for primer in primers:
-	seq=sequences[primers[primer]["chrom"]]
-	for i in range(primers[primer]["start"]-args.scanlen,primers[primer]["start"],1):
-		for j in range(primers[primer]["end"],primers[primer]["end"]+args.scanlen,1):
-			k=int((j-i)/2)
-			if k >= args.flankmax:
-				bsjflank=seq[ j - args.flankmax : j ] + seq[ i : i + args.flankmax ]
-			else:
-				bsjflank=seq[ j-k : j ] + seq[ i : i+k ]
-			sname = "_".join([primer,str(i),str(j)])
-			# print(sname)
-			# print(bsjflank)
-			myseq = HTSeq.Sequence( bytes(offset+bsjflank+offset, 'utf-8'), sname)
-			myseq.write_to_fasta_file(outfastafile)
-outfastafile.close()
\ No newline at end of file
diff --git a/scripts/run_wrapper.bash b/scripts/run_wrapper.bash
deleted file mode 100644
index 155e223..0000000
--- a/scripts/run_wrapper.bash
+++ /dev/null
@@ -1,268 +0,0 @@
-#!/usr/bin/env bash
-# Author: Vishal Koparde, Ph.D.
-# CCBR, NCI
-# (c) 2021
-#
-# wrapper script to run the TOBIAS snakemake workflow
-# run tobias
-# https://github.com/loosolab/tobias/
-# ## clone the pipeline to a folder
-# ## git clone https://github.com/loosolab/TOBIAS.git
-
-set -eo pipefail
-module purge
-
-SINGULARITY_BINDS="-B ${PIPELINE_HOME}:${PIPELINE_HOME} -B ${WORKDIR}:${WORKDIR}"
-
-function get_git_commitid_tag() {
-  cd $1
-  gid=$(git rev-parse HEAD)
-  tag=$(git describe --tags $gid 2>/dev/null)
-  echo -ne "$gid\t$tag"
-}
-
-# ## setting PIPELINE_HOME
-PIPELINE_HOME=$(readlink -f $(dirname "$0"))
-echo "Pipeline Dir: $PIPELINE_HOME"
-SNAKEFILE="${PIPELINE_HOME}/Snakefile"
-# get github commit tag
-GIT_COMMIT_TAG=$(get_git_commitid_tag $PIPELINE_HOME)
-echo "Git Commit/Tag: $GIT_COMMIT_TAG"
-
-function usage() { cat << EOF
-run_tobias.sh: run TOBIAS for ATAC seq data
-USAGE:
-  bash run_tobias.sh <MODE>  <path_to_workdir>
-Required Positional Argument:
-  MODE: [Type: Str] Valid options:
-    a) init <path_to_workdir> : initialize workdir
-    b) run <path_to_workdir>: run with slurm
-    c) reset <path_to_workdir> : DELETE workdir dir and re-init it
-    e) dryrun <path_to_workdir> : dry run snakemake to generate DAG
-    f) unlock <path_to_workdir> : unlock workdir if locked by snakemake
-    g) runlocal <path_to_workdir>: run without submitting to sbatch
-EOF
-}
-
-function err() { cat <<< "
-#
-#
-#
-  $@
-#
-#
-#
-" && usage && exit 1 1>&2; }
-
-function init() {
-
-if [ "$#" -eq "1" ]; then err "init needs an absolute path to the working dir"; fi
-if [ "$#" -gt "2" ]; then err "init takes only one more argument"; fi
-WORKDIR=$2
-x=$(echo $WORKDIR|awk '{print substr($1,1,1)}')
-if [ "$x" != "/" ]; then err "working dir should be supplied as an absolute path"; fi
-echo "Working Dir: $WORKDIR"
-if [ -d $WORKDIR ];then err "Folder $WORKDIR already exists!"; exit 1; fi
-mkdir -p $WORKDIR
-sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/config/config.yaml > $WORKDIR/config.yaml
-
-#create log and stats folders
-if [ ! -d $WORKDIR/logs ]; then mkdir -p $WORKDIR/logs;echo "Logs Dir: $WORKDIR/logs";fi
-if [ ! -d $WORKDIR/stats ];then mkdir -p $WORKDIR/stats;echo "Stats Dir: $WORKDIR/stats";fi
-
-echo "Done Initializing $WORKDIR. You can now edit $WORKDIR/config.yaml and $WORKDIR/samples.tsv"
-
-}
-
-function runcheck(){
-  if [ "$#" -eq "1" ]; then err "absolute path to the working dir needed"; usage; exit 1; fi
-  if [ "$#" -gt "2" ]; then err "too many arguments"; usage; exit 1; fi
-  WORKDIR=$2
-  echo "Working Dir: $WORKDIR"
-  if [ ! -d $WORKDIR ];then err "Folder $WORKDIR does not exist!"; exit 1; fi
-  module load python/3.7
-  module load snakemake/5.24.1
-}
-
-function dryrun() {
-  runcheck "$@"
-  run "--dry-run"
-}
-
-function unlock() {
-  runcheck "$@"
-  run "--unlock"  
-}
-
-function runlocal() {
-  runcheck "$@"
-  if [ "$SLURM_JOB_ID" == "" ];then err "runlocal can only be done on an interactive node"; exit 1; fi
-  module load singularity
-  run "local"
-}
-
-function runslurm() {
-  runcheck "$@"
-  run "slurm"
-}
-
-function preruncleanup() {
-  echo "Running..."
-
-  cd $WORKDIR
-  ## check if initialized
-  for f in config.yaml samples.tsv; do
-    if [ ! -f $WORKDIR/$f ]; then err "Error: '${f}' file not found in workdir ... initialize first!";usage && exit 1;fi
-  done
-  ## Archive previous run files
-  if [ -f ${WORKDIR}/snakemake.log ];then 
-    modtime=$(stat ${WORKDIR}/snakemake.log |grep Modify|awk '{print $2,$3}'|awk -F"." '{print $1}'|sed "s/ //g"|sed "s/-//g"|sed "s/://g")
-    mv ${WORKDIR}/snakemake.log ${WORKDIR}/stats/snakemake.${modtime}.log
-    if [ -f ${WORKDIR}/snakemake.log.HPC_summary.txt ];then 
-      mv ${WORKDIR}/snakemake.log.HPC_summary.txt ${WORKDIR}/stats/snakemake.${modtime}.log.HPC_summary.txt
-    fi
-    if [ -f ${WORKDIR}/snakemake.stats ];then 
-      mv ${WORKDIR}/snakemake.stats ${WORKDIR}/stats/snakemake.${modtime}.stats
-    fi
-  fi
-  nslurmouts=$(find ${WORKDIR} -maxdepth 1 -name "slurm-*.out" |wc -l)
-  if [ "$nslurmouts" != "0" ];then
-    for f in $(ls ${WORKDIR}/slurm-*.out);do gzip -n $f;mv ${f}.gz ${WORKDIR}/logs/;done
-  fi
-
-}
-
-function postrun() {
-  bash ${PIPELINE_HOME}/scripts/gather_cluster_stats.sh ${WORKDIR}/snakemake.log > ${WORKDIR}/snakemake.log.HPC_summary.txt
-}
-
-function run() {
-
-
-  if [ "$1" == "local" ];then
-
-  preruncleanup
-
-  snakemake -s ${PIPELINE_HOME}/$SNAKEFILE \
-  --directory $WORKDIR \
-  --printshellcmds \
-  --use-singularity \
-  --singularity-args $SINGULARITY_BINDS \
-  --use-envmodules \
-  --latency-wait 120 \
-  --configfile ${WORKDIR}/config.yaml \
-  --cores all \
-  --stats ${WORKDIR}/snakemake.stats \
-  2>&1|tee ${WORKDIR}/snakemake.log
-
-  if [ "$?" -eq "0" ];then
-    snakemake -s ${PIPELINE_HOME}/$SNAKEFILE \
-    --report ${WORKDIR}/runlocal_snakemake_report.html \
-    --directory $WORKDIR \
-    --configfile ${WORKDIR}/config.yaml 
-  fi
-
-  postrun
-
-  elif [ "$1" == "slurm" ];then
-  
-  preruncleanup
-
-  cat > ${WORKDIR}/submit_script.sbatch << EOF
-#!/bin/bash
-#SBATCH --job-name="insert_jobname_here"
-#SBATCH --mem=10g
-#SBATCH --partition="ccr,norm"
-#SBATCH --time=96:00:00
-#SBATCH --cpus-per-task=2
-
-module load python/3.7
-module load snakemake/5.24.1
-module load singularity
-
-cd \$SLURM_SUBMIT_DIR
-
-snakemake -s $SNAKEFILE \
---directory $WORKDIR \
---use-singularity \
---singularity-args $SINGULARITY_BINDS \
---use-envmodules \
---printshellcmds \
---latency-wait 120 \
---configfile ${WORKDIR}/config.yaml \
---cluster-config ${PIPELINE_HOME}/config/cluster.json \
---cluster "sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name {cluster.name} --output {cluster.output} --error {cluster.error}" \
--j 500 \
---rerun-incomplete \
---keep-going \
---stats ${WORKDIR}/snakemake.stats \
-2>&1|tee ${WORKDIR}/snakemake.log
-
-if [ "\$?" -eq "0" ];then
-  snakemake -s $SNAKEFILE \
-  --directory $WORKDIR \
-  --report ${WORKDIR}/runslurm_snakemake_report.html \
-  --configfile ${WORKDIR}/config.yaml 
-fi
-
-bash ${PIPELINE_HOME}/scripts/gather_cluster_stats.sh ${WORKDIR}/snakemake.log > ${WORKDIR}/snakemake.log.HPC_summary.txt
-
-EOF
-
-  sbatch ${WORKDIR}/submit_script.sbatch
-
-  else
-
-snakemake $1 -s ${SNAKEFILE} \
---directory $WORKDIR \
---use-envmodules \
---printshellcmds \
---latency-wait 120 \
---configfile ${WORKDIR}/config.yaml \
---cluster-config ${PIPELINE_HOME}/config/cluster.json \
---cluster "sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name {cluster.name} --output {cluster.output} --error {cluster.error}" \
--j 500 \
---rerun-incomplete \
---keep-going \
---stats ${WORKDIR}/snakemake.stats
-
-  fi
-
-}
-
-function reset() {
-if [ "$#" -eq "1" ]; then err "cleanup needs an absolute path to the existing working dir"; usage; fi
-if [ "$#" -gt "2" ]; then err "cleanup takes only one more argument"; usage; fi
-WORKDIR=$2
-echo "Working Dir: $WORKDIR"
-if [ ! -d $WORKDIR ];then err "Folder $WORKDIR does not exist!";fi
-echo "Deleting $WORKDIR"
-rm -rf $WORKDIR
-echo "Re-Initializing $WORKDIR"
-init "$@"
-}
-
-
-function main(){
-
-  if [ $# -eq 0 ]; then usage; exit 1; fi
-
-  case $1 in
-    init) init "$@" && exit 0;;
-    dryrun) dryrun "$@" && exit 0;;
-    unlock) unlock "$@" && exit 0;;
-    run) runslurm "$@" && exit 0;;
-    runlocal) runlocal "$@" && exit 0;;
-    reset) reset "$@" && exit 0;;
-    -h | --help | help) usage && exit 0;;
-    -* | --*) err "Error: Failed to provide mode: <init|run>."; usage && exit 1;;
-    *) err "Error: Failed to provide mode: <init|run>. '${1}' is not supported."; usage && exit 1;;
-  esac
-}
-
-main "$@"
-
-
-
-
-