diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 5573fb6..0000000
--- a/.editorconfig
+++ /dev/null
@@ -1,15 +0,0 @@
-# EditorConfig is awesome: http://EditorConfig.org
-
-# top-most EditorConfig file
-root = true
-
-[*]
-end_of_line = lf
-insert_final_newline = true
-charset = utf-8
-indent_style = space
-indent_size = 4
-
-[*.{yml,yaml}]
-indent_style = space
-indent_size = 2
diff --git a/.gitattributes b/.gitattributes
deleted file mode 100644
index 9440e44..0000000
--- a/.gitattributes
+++ /dev/null
@@ -1,2 +0,0 @@
-*.smk linguist-language=Python
-*.snakefile linguist-language=Python
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index fdb60f6..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,5 +0,0 @@
-**/.koparde*
-!.editorconfig
-!.gitignore
-!.gitattributes
-site/
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index c5caeb8..0000000
--- a/LICENSE
+++ /dev/null
@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2021 Vishal Koparde
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
diff --git a/README.md b/README.md
deleted file mode 100644
index fcd525e..0000000
--- a/README.md
+++ /dev/null
@@ -1,18 +0,0 @@
-![GitHub issues](https://img.shields.io/github/issues/CCBR/CCBR_circRNA_AmpliconSeq)![forks](https://img.shields.io/github/forks/CCBR/CCBR_circRNA_AmpliconSeq)![stars](https://img.shields.io/github/stars/CCBR/CCBR_circRNA_AmpliconSeq)![LICENSE](https://img.shields.io/github/license/CCBR/CCBR_circRNA_AmpliconSeq)
-
-# CCBR circRNA AmpliconSeq Snakemake Workflow
-This is a snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers. Some basic usage instructions are as follows:
-
-```
-USAGE:
-  bash ./run_circRNA_AmpliconSeq -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
-Required Arguments:
-1.  RUNMODE: [Type: String] Valid options:
-    *) init : initialize workdir
-    *) run : run with slurm
-    *) reset : DELETE workdir dir and re-init it
-    *) dryrun : dry run snakemake to generate DAG
-    *) unlock : unlock workdir if locked by snakemake
-    *) runlocal : run without submitting to sbatch
-2.  WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.
-```
diff --git a/config/cluster.json b/config/cluster.json
deleted file mode 100644
index 9307f82..0000000
--- a/config/cluster.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    "__default__": {
-        "gres": "lscratch:256",
-        "mem": "20g",
-        "partition": "ccr", "qos": "ccrcore",
-        "threads": "2",
-        "time": "4:00:00",
-        "name"      : "{rule}.{wildcards}",
-        "output"    : "logs/${{SLURM_JOBID}}.%j.{rule}.{wildcards}.out",
-        "error"     : "logs/${{SLURM_JOBID}}.%j.{rule}.{wildcards}.err"
-    },
-	"align":{
-        "mem": "120g",
-        "threads": "56",
-        "time": "48:00:00"		
-	},
-	"cutadapt":{
-        "mem": "120g",
-        "threads": "56",
-        "time": "48:00:00"		
-	}
-}
diff --git a/config/config.yaml b/config/config.yaml
deleted file mode 100644
index bd2cb79..0000000
--- a/config/config.yaml
+++ /dev/null
@@ -1,68 +0,0 @@
-## you probably need to change or comment/uncomment some of these
-#
-# The working dir... output will be in the results subfolder of the workdir
-workdir: "WORKDIR"
-#
-# tab delimited samples file ... should have the following 3 columns
-# sampleName	path_to_R1_fastq	path_to_R2_fastq
-#
-samples: "WORKDIR/samples.tsv"
-#
-# BSJ fasta file
-# bsjfa: "/data/Ziegelbauer_lab/Sarah/MiSeq_R2/bsjs_020921.fasta"
-#
-# divergent primers information TSV file which will be converted to BED6 format
-# The columns in this files are (see example at the bottom):
-# Primer	Chromosome	Start	End	Strand	PrimerSequence_5prime_to_3prime	Reference
-primertsv: "PIPELINE_HOME/resources/primers.tsv"
-# primerbed: "PIPELINE_HOME/resources/primers.bed"
-reffa: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.fa"
-#
-bowtie2_alignment_parameters: "--very-sensitive-local"
-salmon_parameters: "-l U --maxReadOcc 3 --minAssignedFrags 60"
-aggregate_quant_rowsum_filter: 50     # aggregate quant.sf across samples and filter out rows <= this filter value
-#
-#
-#
-#
-#
-#
-## you most probably dont need to change these
-scriptsdir: "PIPELINE_HOME/workflow/scripts"
-resourcesdir: "PIPELINE_HOME/resources"
-tools: "PIPELINE_HOME/config/tools.yaml"
-cluster: "PIPELINE_HOME/config/cluster.json"
-adapters: "PIPELINE_HOME/resources/TruSeq_and_nextera_adapters.consolidated.fa"
-# bsjfadefault: "PIPELINE_HOME/resources/bsjs_020921.fasta.gz"
-#
-## Resources
-#
-# hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC
-#
-# ref_fa: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.fa"
-# ref_gtf: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.gtf"
-# regions: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.fa.regions"
-# star_index_dir: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/STAR_index_no_GTF_2.7.6a"
-# ref_bwa_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC"
-# ref_hisat_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC"
-# ref_bowtie1_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC"
-# genepred_w_geneid: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.genes.genepred_w_geneid"
-#
-
-# Primer	Chromosome	Start	End	Strand	PrimerSequence_5prime_to_3prime	Reference
-# circ29_F	NC_009333.1	29751	29770	+	ACCAGACGGCAAGGTTTTTA	https://doi.org/10.1073/pnas.1816183115
-# circ29_R	NC_009333.1	29641	29663	-	TCGTTAGTCAACCTAGCAAAACA	https://doi.org/10.1073/pnas.1816183115
-# circ57_F	NC_009333.1	57271	57290	+	CAACCAAAAGGCAGAGTCGT	https://doi.org/10.1073/pnas.1816183115
-# circ57_R	NC_009333.1	57057	57076	-	GGCTGAACCCAAGAACTTCA	https://doi.org/10.1073/pnas.1816183115
-# circvIRF4_F	NC_009333.1	88288	88307	-	CTCCGTGTGGATACCAGTGA	10.1128/JVI.01952-18
-# circvIRF4_R	NC_009333.1	88746	88764	+	TGGTTCCACGCAACAGTCT	10.1128/JVI.01952-18
-# circ97_F	NC_009333.1	98176	98195	-	GGAAGAAGCTCATGGACTGG	https://doi.org/10.1073/pnas.1816183115
-# circ97_R	NC_009333.1	97964	97983	+	GACCTAAAAACCCGGAGGAG	https://doi.org/10.1073/pnas.1816183115
-# circT0.7_F3	NC_009333.1	118221	118240	+	AGTGAGGAGGGAGGAGGGCA
-# circT0.7_R2	NC_009333.1	117701	117722	-	CGCTCTCCCAAACCACACGAAT
-# circORF72_F3	NC_009333.1	123582	123601	+	AAGATTAAGGGCCAACGCGA
-# circORF72_R1	NC_009333.1	123138	123157	-	TAGTTCCTCAGCTGGCAAGC
-# circ1400_F	chr4	37631449	37631468	-	ATGTCTGTTAGTGGGGCTGA	https://doi.org/10.1073/pnas.1816183115
-# circ1400_R	chr4	37638469	37638488	+	TATCTGCTACCATCGCCTTT	https://doi.org/10.1073/pnas.1816183115
-# circ1741_F	chr7	129015044	129015063	-	TCGTTCCTTACGAATTGGAG	https://doi.org/10.1073/pnas.1816183115
-# circ1741_R	chr7	129018113	129018132	+	CTGCCGGATCTGTAACAACT	https://doi.org/10.1073/pnas.1816183115
\ No newline at end of file
diff --git a/config/samples.1.tsv b/config/samples.1.tsv
deleted file mode 100644
index e8580f4..0000000
--- a/config/samples.1.tsv
+++ /dev/null
@@ -1,25 +0,0 @@
-sampleName	path_to_R1_fastq	path_to_R2_fastq
-iSLK_KO_c1400	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1400/iSLK_KO_c1400_S15_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1400/iSLK_KO_c1400_S15_R2_001.fastq.gz
-iSLK_KO_c1741	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1741/iSLK_KO_c1741_S16_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1741/iSLK_KO_c1741_S16_R2_001.fastq.gz
-iSLK_KO_kcirc29	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_kcirc29/iSLK_KO_kcirc29_S9_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_kcirc29/iSLK_KO_kcirc29_S9_R2_001.fastq.gz
-iSLK_KO_kcirc57	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_kcirc57/iSLK_KO_kcirc57_S10_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_kcirc57/iSLK_KO_kcirc57_S10_R2_001.fastq.gz
-iSLK_KO_kcirc97	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_kcirc97/iSLK_KO_kcirc97_S11_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_kcirc97/iSLK_KO_kcirc97_S11_R2_001.fastq.gz
-iSLK_KO_ORF72	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_ORF72/iSLK_KO_ORF72_S13_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_ORF72/iSLK_KO_ORF72_S13_R2_001.fastq.gz
-iSLK_KO_T0_7	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_T0_7/iSLK_KO_T0_7_S14_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_T0_7/iSLK_KO_T0_7_S14_R2_001.fastq.gz
-iSLK_KO_vIRF4	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_vIRF4/iSLK_KO_vIRF4_S12_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_vIRF4/iSLK_KO_vIRF4_S12_R2_001.fastq.gz
-iSLK_WT_c1400	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_c1400/iSLK_WT_c1400_S7_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_c1400/iSLK_WT_c1400_S7_R2_001.fastq.gz
-iSLK_WT_c1741	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_c1741/iSLK_WT_c1741_S8_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_c1741/iSLK_WT_c1741_S8_R2_001.fastq.gz
-iSLK_WT_kcirc29	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_kcirc29/iSLK_WT_kcirc29_S1_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_kcirc29/iSLK_WT_kcirc29_S1_R2_001.fastq.gz
-iSLK_WT_kcirc57	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_kcirc57/iSLK_WT_kcirc57_S2_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_kcirc57/iSLK_WT_kcirc57_S2_R2_001.fastq.gz
-iSLK_WT_kcirc97	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_kcirc97/iSLK_WT_kcirc97_S3_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_kcirc97/iSLK_WT_kcirc97_S3_R2_001.fastq.gz
-iSLK_WT_ORF72	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_ORF72/iSLK_WT_ORF72_S5_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_ORF72/iSLK_WT_ORF72_S5_R2_001.fastq.gz
-iSLK_WT_T0_7	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_T0_7/iSLK_WT_T0_7_S6_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_T0_7/iSLK_WT_T0_7_S6_R2_001.fastq.gz
-iSLK_WT_vIRF4	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_vIRF4/iSLK_WT_vIRF4_S4_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_WT_vIRF4/iSLK_WT_vIRF4_S4_R2_001.fastq.gz
-LEC_BAC16_c1400	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_c1400/LEC_BAC16_c1400_S23_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_c1400/LEC_BAC16_c1400_S23_R2_001.fastq.gz
-LEC_BAC16_c1741	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_c1741/LEC_BAC16_c1741_S24_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_c1741/LEC_BAC16_c1741_S24_R2_001.fastq.gz
-LEC_BAC16_kcirc29	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_kcirc29/LEC_BAC16_kcirc29_S17_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_kcirc29/LEC_BAC16_kcirc29_S17_R2_001.fastq.gz
-LEC_BAC16_kcirc57	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_kcirc57/LEC_BAC16_kcirc57_S18_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_kcirc57/LEC_BAC16_kcirc57_S18_R2_001.fastq.gz
-LEC_BAC16_kcirc97	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_kcirc97/LEC_BAC16_kcirc97_S19_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_kcirc97/LEC_BAC16_kcirc97_S19_R2_001.fastq.gz
-LEC_BAC16_ORF72	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_ORF72/LEC_BAC16_ORF72_S21_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_ORF72/LEC_BAC16_ORF72_S21_R2_001.fastq.gz
-LEC_BAC16_T0_7	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_T0_7/LEC_BAC16_T0_7_S22_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_T0_7/LEC_BAC16_T0_7_S22_R2_001.fastq.gz
-LEC_BAC16_vIRF4	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_vIRF4/LEC_BAC16_vIRF4_S20_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_LEC_BAC16_vIRF4/LEC_BAC16_vIRF4_S20_R2_001.fastq.gz
diff --git a/config/samples.tsv b/config/samples.tsv
deleted file mode 100644
index 2bf83b7..0000000
--- a/config/samples.tsv
+++ /dev/null
@@ -1,2 +0,0 @@
-sampleName	path_to_R1_fastq	path_to_R2_fastq
-iSLK_KO_c1741	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1741/iSLK_KO_c1741_S16_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1741/iSLK_KO_c1741_S16_R2_001.fastq.gz
\ No newline at end of file
diff --git a/config/samples.tsv.testing b/config/samples.tsv.testing
deleted file mode 100644
index 2bf83b7..0000000
--- a/config/samples.tsv.testing
+++ /dev/null
@@ -1,2 +0,0 @@
-sampleName	path_to_R1_fastq	path_to_R2_fastq
-iSLK_KO_c1741	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1741/iSLK_KO_c1741_S16_R1_001.fastq.gz	/data/Ziegelbauer_lab/Sarah/MiSeq_R2/Flowcell_000000000-JBHWF/Sample_iSLK_KO_c1741/iSLK_KO_c1741_S16_R2_001.fastq.gz
\ No newline at end of file
diff --git a/config/tools.yaml b/config/tools.yaml
deleted file mode 100644
index 4cb565b..0000000
--- a/config/tools.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
-bowtie2:
- version: "bowtie/2-2.4.2"
-cutadapt:
- version: "cutadapt/1.18"
-# fastqc:
-#  version: "fastqc/0.11.9"
-# hisat:
-#  version: "hisat/2.2.1.0"
-# multiqc:
-#  version: "multiqc/1.9"
-# picard:
-#  version: "picard/2.25.0"
-python37:
- version: "python/3.7"
-salmon:
- version: "salmon/1.4.0"
-sambamba:
- version: "sambamba/0.8.0"
-R:
- version: "R/4.0.3"
-# samtools:
-#  version: "samtools/1.11"
-# star:
-#  version: "STAR/2.7.6a"
-#  alignTranscriptsPerReadNmax: "20000"
-# stringtie:
-#  version: "stringtie/2.1.4"
-# ucsc:
-#  version: "ucsc/407"
diff --git a/docs/index.md b/docs/index.md
deleted file mode 100644
index e69de29..0000000
diff --git a/index.html b/index.html
new file mode 100644
index 0000000..fddf223
--- /dev/null
+++ b/index.html
@@ -0,0 +1,8 @@
+<html xmlns="http://www.w3.org/1999/xhtml">    
+  <head>      
+    <title>Redirect to CCBR/CCBR_circRNA_AmpliconSeq</title>      
+    <meta http-equiv="refresh" content="0;URL='https://github.com/CCBR/CCBR_circRNA_AmpliconSeq/'" />    
+  </head>    
+  <body> 
+  </body>  
+</html>  
\ No newline at end of file
diff --git a/mkdocs.yaml b/mkdocs.yaml
deleted file mode 100644
index 5aeb0cd..0000000
--- a/mkdocs.yaml
+++ /dev/null
@@ -1,36 +0,0 @@
-# Project Information
-site_name: circRNA ampliconSeq
-site_author: Vishal Koparde, Ph.D.
-# Repository
-repo_name: CCBR/CCBR_circRNA_AmpliconSeq
-repo_url: https://github.com/CCBR/CCBR_circRNA_AmpliconSeq
-
-# Copyright
-copyright: Copyright &copy; 2021 CCBR
-
-# Configuration
-theme:
-  name: material
-  palette:
-    scheme: default
-
-plugins:
-  - search
-
-# Customization
-extra:
-  social:
-    - icon: fontawesome/solid/users
-      link: http://bioinformatics.cancer.gov
-    - icon: fontawesome/brands/github
-      link: https://github.com/CCBR
-    - icon: fontawesome/brands/docker
-      link: https://hub.docker.com/orgs/nciccbr/repositories
-
-# Page Tree
-nav:
-  - Home: index.md
-  - Flowchart: flowchart.md
-  - Tutorial: tutorial.md
-  - References: references.md
-  - Versions: versions.md
diff --git a/resources/TruSeq_and_nextera_adapters.consolidated.fa b/resources/TruSeq_and_nextera_adapters.consolidated.fa
deleted file mode 100755
index de67830..0000000
--- a/resources/TruSeq_and_nextera_adapters.consolidated.fa
+++ /dev/null
@@ -1,94 +0,0 @@
->Nextera_PrefixNX/1
-AGATGTGTATAAGAGACAG
->Nextera_Trans1
-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
->Nextera_Trans1_rc
-CTGTCTCTTATACACATCTGACGCTGCCGACGA
->Nextera_Trans2
-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
->Nextera_Trans2_rc
-CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
->TruSeq3_PE1
-TACACTCTTTCCCTACACGACGCTCTTCCGATCT
->TruSeq3_PE1_rc
-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
->TruSeq3_PE2
-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
->TruSeq3_PE2_rc
-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
->TruSeq_Small_RNA
-TGGAATTCTCGGGTGCCAAGG
->NEB_miRNA_3primeACTGTAGGCACCATCAAT/AACTGTAGGCACCATCAAT
-AGATCGGAAGAGCACACGTCT
->Illumina_Single_End_Adapter_1
-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
->Illumina_Single_End_Adapter_2
-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
->Illumina_Paired_End_Adapter_2
-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
->Illumina_Paired_End_PCR_Primer_2
-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
->Illumina_Paired_End_Sequencing_Primer_2
-CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
->Illumina_DpnII_expression_Adapter_1
-ACAGGTTCAGAGTTCTACAGTCCGAC
->Illumina_DpnII_expression_PCR_Primer_1
-CAAGCAGAAGACGGCATACGA
->Illumina_DpnII_expression_PCR_Primer_2
-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
->Illumina_NlaIII_expression_Adapter_1
-ACAGGTTCAGAGTTCTACAGTCCGACATG
->Illumina_NlaIII_expression_Sequencing_Primer
-CCGACAGGTTCAGAGTTCTACAGTCCGACATG
->Illumina_Multiplexing_Adapter_1
-GATCGGAAGAGCACACGTCT
->Illumina_Multiplexing_Index_Sequencing_Primer
-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
->Illumina_PCR_Primer_Index
-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTC
->Illumina_DpnII_Gex_Adapter_1
-GATCGTCGGACTGTAGAACTCTGAAC
->Illumina_DpnII_Gex_Adapter_2.01
-TCGTATGCCGTCTTCTGCTTG
->Illumina_DpnII_Gex_Sequencing_Primer
-CGACAGGTTCAGAGTTCTACAGTCCGACGATC
->Illumina_NlaIII_Gex_Adapter_1.01
-TCGGACTGTAGAACTCTGAAC
->Illumina_Small_RNA_3p_Adapter_1
-ATCTCGTATGCCGTCTTCTGCTTG
->TruSeq_Universal_Adapter
-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
->TruSeq_Adapter,_Indices
-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNTCTCGTATGCCGTCTTCTGCTTG
->Illumina_RNA_RT_Primer
-GCCTTGGCACCCGAGAATTCCA
->Illumina_RNA_PCR_Primer
-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
->RNA_PCR_Primer_Indices
-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
->Illumina_Universal_Adapter
-AGATCGGAAGAG
->Illumina_Small_RNA_3'_Adapter
-TGGAATTCTCGG
->Illumina_Small_RNA_5'_Adapter
-GATCGTCGGACT
->Nextera_Transposase_Sequence
-CTGTCTCTTATA
->NEB_miRNA_5prime
-GTTCAGAGTTCTACAGTCCGACGATC
->Qiagen_miRNA_5prime
-GTTCAGAGTTCTACAGTCCGACGATC
->Qiagen_miRNA_3prime
-AACTGTAGGCACCATCAAT
->PolyA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
->PolyC
-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
->PolyG
-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
->PolyT
-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
->Barcode_Index25_F
-ACTGAT
->Barcode_Index25_R
-ATCAGT
\ No newline at end of file
diff --git a/resources/bsjs_020921.fasta.gz b/resources/bsjs_020921.fasta.gz
deleted file mode 100644
index 4c51520..0000000
Binary files a/resources/bsjs_020921.fasta.gz and /dev/null differ
diff --git a/resources/primers.bed b/resources/primers.bed
deleted file mode 100644
index 53895fe..0000000
--- a/resources/primers.bed
+++ /dev/null
@@ -1,16 +0,0 @@
-NC_009333.1	29751	29770	circ29_F	.	+
-NC_009333.1	29641	29663	circ29_R	.	-
-NC_009333.1	57271	57290	circ57_F	.	+
-NC_009333.1	57057	57076	circ57_R	.	-
-NC_009333.1	88288	88307	circvIRF4_F	.	-
-NC_009333.1	88746	88764	circvIRF4_R	.	+
-NC_009333.1	98176	98195	circ97_F	.	-
-NC_009333.1	97964	97983	circ97_R	.	+
-NC_009333.1	118221	118240	circT0.7_F3	.	+
-NC_009333.1	117701	117722	circT0.7_R2	.	-
-NC_009333.1	123582	123601	circORF72_F3	.	+
-NC_009333.1	123138	123157	circORF72_R1	.	-
-chr4	37631449	37631468	circ1400_F	.	-
-chr4	37638469	37638488	circ1400_R	.	+
-chr7	129015044	129015063	circ1741_F	.	-
-chr7	129018113	129018132	circ1741_R	.	+
diff --git a/resources/primers.tsv b/resources/primers.tsv
deleted file mode 100644
index 4c33ca6..0000000
--- a/resources/primers.tsv
+++ /dev/null
@@ -1,17 +0,0 @@
-Primer	Chromosome	Start	End	Strand	PrimerSequence_5prime_to_3prime	Reference
-circ29_F	NC_009333.1	29751	29770	+	ACCAGACGGCAAGGTTTTTA	https://doi.org/10.1073/pnas.1816183115
-circ29_R	NC_009333.1	29641	29663	-	TCGTTAGTCAACCTAGCAAAACA	https://doi.org/10.1073/pnas.1816183115
-circ57_F	NC_009333.1	57271	57290	+	CAACCAAAAGGCAGAGTCGT	https://doi.org/10.1073/pnas.1816183115
-circ57_R	NC_009333.1	57057	57076	-	GGCTGAACCCAAGAACTTCA	https://doi.org/10.1073/pnas.1816183115
-circvIRF4_F	NC_009333.1	88288	88307	-	CTCCGTGTGGATACCAGTGA	10.1128/JVI.01952-18
-circvIRF4_R	NC_009333.1	88746	88764	+	TGGTTCCACGCAACAGTCT	10.1128/JVI.01952-18
-circ97_F	NC_009333.1	98176	98195	-	GGAAGAAGCTCATGGACTGG	https://doi.org/10.1073/pnas.1816183115
-circ97_R	NC_009333.1	97964	97983	+	GACCTAAAAACCCGGAGGAG	https://doi.org/10.1073/pnas.1816183115
-circT0.7_F3	NC_009333.1	118221	118240	+	AGTGAGGAGGGAGGAGGGCA	
-circT0.7_R2	NC_009333.1	117701	117722	-	CGCTCTCCCAAACCACACGAAT	
-circORF72_F3	NC_009333.1	123582	123601	+	AAGATTAAGGGCCAACGCGA	
-circORF72_R1	NC_009333.1	123138	123157	-	TAGTTCCTCAGCTGGCAAGC	
-circ1400_F	chr4	37631449	37631468	-	ATGTCTGTTAGTGGGGCTGA	https://doi.org/10.1073/pnas.1816183115
-circ1400_R	chr4	37638469	37638488	+	TATCTGCTACCATCGCCTTT	https://doi.org/10.1073/pnas.1816183115
-circ1741_F	chr7	129015044	129015063	-	TCGTTCCTTACGAATTGGAG	https://doi.org/10.1073/pnas.1816183115
-circ1741_R	chr7	129018113	129018132	+	CTGCCGGATCTGTAACAACT	https://doi.org/10.1073/pnas.1816183115
diff --git a/run_circRNA_AmpliconSeq b/run_circRNA_AmpliconSeq
deleted file mode 100755
index 6274795..0000000
--- a/run_circRNA_AmpliconSeq
+++ /dev/null
@@ -1,303 +0,0 @@
-#!/usr/bin/env bash
-# Author: Vishal Koparde, Ph.D.
-# CCBR, NCI
-# (c) 2021
-#
-# wrapper script to run the circRNA AmpliconSeq pipeline
-#
-# 
-# https://github.com/CCBR/CCBR_circRNA_AmpliconSeq
-
-set -eo pipefail
-module purge
-
-SCRIPTNAME="$0"
-SCRIPTDIRNAME=$(readlink -f $(dirname $0))
-SCRIPTBASENAME=$(readlink -f $(basename $0))
-
-EXTRA_SINGULARITY_BINDS="-B /data/CCBR_Pipeliner/:/data/CCBR_Pipeliner/ -B /data/Ziegelbauer_lab/resources/:/data/Ziegelbauer_lab/resources/"
-
-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: $PIPELINE_HOME"
-# set snakefile
-SNAKEFILE="${PIPELINE_HOME}/workflow/Snakefile"
-
-# get github commit tag
-GIT_COMMIT_TAG=$(get_git_commitid_tag $PIPELINE_HOME)
-echo "Git Commit/Tag: $GIT_COMMIT_TAG"
-
-function usage() { cat << EOF
-
-${SCRIPTBASENAME}
---> run circRNA AmpliconSeq Pipeline
-
-USAGE:
-  bash ${SCRIPTNAME} -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
-Required Arguments:
-1.  RUNMODE: [Type: String] Valid options:
-    *) init : initialize workdir
-    *) run : run with slurm
-    *) reset : DELETE workdir dir and re-init it
-    *) dryrun : dry run snakemake to generate DAG
-    *) unlock : unlock workdir if locked by snakemake
-    *) runlocal : run without submitting to sbatch
-2.  WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.
-EOF
-}
-
-function err() { cat <<< "
-#
-#
-#
-  $@
-#
-#
-#
-" && usage && exit 1 1>&2; }
-
-
-function init() {
-
-# create output folder
-if [ -d $WORKDIR ];then err "Folder $WORKDIR already exists!"; fi
-mkdir -p $WORKDIR
-
-# copy config and samples files
-sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/config/config.yaml > $WORKDIR/config.yaml
-cp ${PIPELINE_HOME}/config/samples.tsv $WORKDIR/
-
-#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 check_essential_files() {
-  if [ ! -d $WORKDIR ];then err "Folder $WORKDIR does not exist!"; fi
-  for f in config.yaml samples.tsv; do
-    if [ ! -f $WORKDIR/$f ]; then err "Error: '${f}' file not found in workdir ... initialize first!";fi
-  done
-}
-
-function reconfig(){
-  # rebuild config file and replace the config.yaml in the WORKDIR
-  # this is only for dev purposes when new key-value pairs are being added to the config file
-  check_essential_files
-  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/config/config.yaml > $WORKDIR/config.yaml
-  echo "$WORKDIR/config.yaml has been updated!"
-}
-
-function runcheck(){
-  check_essential_files
-  module load python/3.7
-  module load snakemake/5.24.1
-  SINGULARITY_BINDS="$EXTRA_SINGULARITY_BINDS -B ${PIPELINE_HOME}:${PIPELINE_HOME} -B ${WORKDIR}:${WORKDIR}"
-}
-
-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"; fi
-  module load singularity
-  run "local"
-}
-
-function runslurm() {
-  runcheck
-  run "slurm"
-}
-
-function preruncleanup() {
-  echo "Running..."
-
-  # check initialization
-  check_essential_files 
-
-  cd $WORKDIR
-  ## 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 mv ${f} ${WORKDIR}/logs/;done
-  fi
-
-}
-
-
-function run() {
-
-
-  if [ "$1" == "local" ];then
-
-  preruncleanup
-
-  snakemake -s $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 $SNAKEFILE \
-    --report ${WORKDIR}/runlocal_snakemake_report.html \
-    --directory $WORKDIR \
-    --configfile ${WORKDIR}/config.yaml 
-  fi
-
-  elif [ "$1" == "slurm" ];then
-  
-  preruncleanup
-
-  cat > ${WORKDIR}/submit_script.sbatch << EOF
-#!/bin/bash
-#SBATCH --job-name="circRNA_ampliconseq"
-#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} --qos={cluster.qos}" \
--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 <(curl https://raw.githubusercontent.com/CCBR/Tools/master/Biowulf/gather_cluster_stats.sh 2>/dev/null) ${WORKDIR}/snakemake.log > ${WORKDIR}/snakemake.log.HPC_summary.txt
-
-EOF
-
-  sbatch ${WORKDIR}/submit_script.sbatch
-
-  else # for unlock and dryrun 
-
-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() {
-  #delete the workdir and re-initialize it
-  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 [ $# -eq 0 ]; then usage; exit 1; fi
-
-  for i in "$@"
-  do
-  case $i in
-      -m=*|--runmode=*)
-        RUNMODE="${i#*=}"
-      ;;
-      -w=*|--workdir=*)
-        WORKDIR="${i#*=}"
-      ;;
-      *)
-        err "Unknown argument!"    # unknown option
-      ;;
-  esac
-  done
-  WORKDIR=$(readlink -f "$WORKDIR")
-  echo "Working Dir: $WORKDIR"
-  # echo SCRIPTNAME = ${SCRIPTNAME}
-  # echo RUNMODE = ${RUNMODE}
-  # echo WORKDIR = ${WORKDIR}
-  # exit;
-
-
-  case $RUNMODE in
-    init) init && exit 0;;
-    dryrun) dryrun && exit 0;;
-    unlock) unlock && exit 0;;
-    run) runslurm && exit 0;;
-    runlocal) runlocal && exit 0;;
-    reset) reset && exit 0;;
-    dry) dryrun && exit 0;;                      # hidden option
-    local) runlocal && exit 0;;                  # hidden option
-    reconfig) reconfig && exit 0;;               # hidden option for debugging
-    *) err "Unknown RUNMODE \"$RUNMODE\"";;
-  esac
-}
-
-main "$@"
-
-
-
-
-
diff --git a/workflow/Snakefile b/workflow/Snakefile
deleted file mode 100644
index f99ab8b..0000000
--- a/workflow/Snakefile
+++ /dev/null
@@ -1,26 +0,0 @@
-from snakemake.utils import min_version
-min_version("5.24.1")
-
-from os.path import join
-
-include: join("rules/init.smk")
-include: join("rules/trim.smk")
-include: join("rules/align.smk")
-include: join("rules/quant.smk")
-
-
-localrules: all
-
-rule all:
-    input:
-        #trim
-        expand(join(WORKDIR,"results","{sample}","trim","{sample}.R1.trim.fastq.gz"),sample=SAMPLES),
-        expand(join(WORKDIR,"results","{sample}","trim","{sample}.R2.trim.fastq.gz"),sample=SAMPLES),
-        #align
-        expand(join(WORKDIR,"results","{sample}","bam","{sample}.bam"),sample=SAMPLES),
-        #quant
-        join(WORKDIR,"results","mergedquant.tsv"),
-        join(WORKDIR,"results","mergedquant.filtered.tsv")
-        
-
-
diff --git a/workflow/envs/dummy_env.yaml b/workflow/envs/dummy_env.yaml
deleted file mode 100644
index e69de29..0000000
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
deleted file mode 100644
index 70e09e1..0000000
--- a/workflow/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/workflow/rules/init.smk b/workflow/rules/init.smk
deleted file mode 100644
index fb87a25..0000000
--- a/workflow/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/workflow/rules/quant.smk b/workflow/rules/quant.smk
deleted file mode 100644
index 0e85878..0000000
--- a/workflow/rules/quant.smk
+++ /dev/null
@@ -1,53 +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 $outdir
-"""
-
-rule aggregate_quant:
-    input:
-        expand(join(WORKDIR,"results","{sample}","salmon","quant.sf"),sample=SAMPLES)
-    output:
-        mergedquant=join(WORKDIR,"results","mergedquant.tsv"),
-        filteredmergedquant=join(WORKDIR,"results","mergedquant.filtered.tsv")
-    params:
-        rowsumfilter=config['aggregate_quant_rowsum_filter'],
-        plotsdir=join(WORKDIR,"results","pieplots"),
-        rscript=join(SCRIPTSDIR,"pie_plots.R")
-    envmodules: TOOLS["salmon"]["version"],TOOLS["R"]["version"]
-    shell:"""
-names=""
-quants=""
-for i in {input};do
-    outdir=$(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}
-if [ -d {params.plotsdir} ];then rm -rf {params.plotsdir};fi && mkdir {params.plotsdir} && cd {params.plotsdir} && cp {output.filteredmergedquant} . && \
-Rscript {params.rscript} $(basename {output.filteredmergedquant}) && rm -f $(basename {output.filteredmergedquant})
-"""
-
-
-    
\ No newline at end of file
diff --git a/workflow/rules/trim.smk b/workflow/rules/trim.smk
deleted file mode 100644
index 9fe2ff5..0000000
--- a/workflow/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/workflow/scripts/build_primer_bed.py b/workflow/scripts/build_primer_bed.py
deleted file mode 100644
index bebc7f2..0000000
--- a/workflow/scripts/build_primer_bed.py
+++ /dev/null
@@ -1,35 +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
-		primers[circRNAname]["ftype"]=circRNAnamesplit[-1]
-		if strand == "+":
-			primers[circRNAname]["ASorSS"]="SS"
-		elif strand == "-":
-			primers[circRNAname]["ASorSS"]="AS"
-	elif ForR == "R":
-		primers[circRNAname]["rtype"]=circRNAnamesplit[-1]
-for primer in primers:
-	sname=primer+"_"+primers[primer]["ftype"]+primers[primer]["rtype"]+"##"+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/workflow/scripts/gather_cluster_stats.sh b/workflow/scripts/gather_cluster_stats.sh
deleted file mode 100644
index 49c326e..0000000
--- a/workflow/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/workflow/scripts/generate_bsj_fasta_from_primer_bed.py b/workflow/scripts/generate_bsj_fasta_from_primer_bed.py
deleted file mode 100644
index f164634..0000000
--- a/workflow/scripts/generate_bsj_fasta_from_primer_bed.py
+++ /dev/null
@@ -1,106 +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
-
-def complement(c):
-	if c=="A":
-		return "T"
-	elif c=="C":
-		return "G"
-	elif c=="G":
-		return "C"
-	elif c=="T":
-		return "A"
-	elif c=="N":
-		return "N"
-	else:
-		print("Unknown char %s. expecting A,C,G,T or N"%(c))
-		exit()
-
-def revcom(seq):
-	rc=seq[::-1].upper()
-	rc="".join(list(map(lambda x:complement(x),rc)))
-	return rc
-
-def convertnt(c):
-	if c=="A":
-		return "1"
-	elif c=="C":
-		return "4"
-	elif c=="G":
-		return "3"
-	elif c=="T":
-		return "2"
-	elif c=="N":
-		return "0"
-	else:
-		return "-1"
-
-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), name is expected to have _AS/_SS suffix')
-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:
-	ASorSS=primer.split("##")[-1]
-	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:
-				bsjflanka=seq[ j - args.flankmax : j ]
-				bsjflankb=seq[ i : i + args.flankmax ]
-			else:
-				bsjflanka=seq[ j-k : j ]
-				bsjflankb=seq[ i : i+k ]
-			if ASorSS == "SS":
-				five_da=bsjflanka[-2:]+"-"+seq[j:j+2]
-				three_da=seq[i-2:i]+"-"+bsjflankb[:2]
-				da=seq[j:j+2]+"-"+seq[i-2:i]
-			elif ASorSS == "AS":
-				five_da=revcom(seq[i-2:i])+"-"+revcom(bsjflankb[:2])
-				three_da=revcom(bsjflanka[-2:])+"-"+revcom(seq[j:j+2])
-				da=revcom(seq[i-2:i])+"-"+revcom(seq[j:j+2])
-			else:
-				print("Primer %s does not have AS or SS suffix"%(primer))
-				exit()
-			bsjflank=bsjflanka+bsjflankb
-			bsjflank=bsjflank.upper()
-			bsjflank_nt="".join(list(map(lambda x:convertnt(x),bsjflank)))				
-			sname = "##".join([primer,primers[primer]["chrom"],str(i),str(j),five_da,three_da,da,bsjflank_nt])
-			# print(sname)
-			# print(bsjflank)
-			myseq = HTSeq.Sequence( bytes(offset+bsjflank+offset, 'utf-8'), sname)
-			myseq.write_to_fasta_file(outfastafile)
-outfastafile.close()
-
diff --git a/workflow/scripts/get_donor_acceptor_from_salmon_quant.py b/workflow/scripts/get_donor_acceptor_from_salmon_quant.py
deleted file mode 100644
index 7640899..0000000
--- a/workflow/scripts/get_donor_acceptor_from_salmon_quant.py
+++ /dev/null
@@ -1,34 +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) name is expected to have _AS/_SS suffix')
-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)
\ No newline at end of file
diff --git a/workflow/scripts/pie_plots.R b/workflow/scripts/pie_plots.R
deleted file mode 100644
index 2f32303..0000000
--- a/workflow/scripts/pie_plots.R
+++ /dev/null
@@ -1,95 +0,0 @@
-
-rm(list=ls())
-library("tidyverse")
-library("RColorBrewer")
-n <- 101
-qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
-col_vector = unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
-
-read_data_table <-function(fname,circRNA){
-  d=read.csv(fname,sep="\t",header=TRUE)
-  samplelist=colnames(d)[2:length(colnames(d))]
-  d %>% separate(col="Name",into=c("circRNA","ASorSS","start","end","fiveDA","threeDA","DA","NT"),sep="##") -> d
-  d$fiveDA=NULL
-  d$threeDA=NULL
-  x=list()
-  x[["table"]]=d
-  x[["samplelist"]]=samplelist
-  x[["circRNAlist"]]=unique(d$circRNA)
-  return(x)
-}
-filter_table_by_cname <-function(d,circRNA){
-  k=d$circRNA==circRNA
-  d=d[k,]
-  return(d)
-}
-filter_table_by_sname <-function(d,samplename){
-  d=data.frame(DA=d$DA,counts=d[[samplename]])
-  d=d[order(d$counts,decreasing = TRUE),]
-  d=d[!(d$counts==0),]
-  return(d)
-}
-add_perc_sign <- function(s){
-  result=""
-  if (as.character(s)!=""){
-    result=paste0(as.character(s),"%")
-  }
-  return(result)
-}
-
-create_perc_table<-function(df){
-  table_percent <- df %>% mutate(DA=DA,perc = round((counts/ sum(counts)) * 100, 1)) %>%
-    mutate(DA=DA,labels=perc,y_text=cumsum(perc)-perc/2)
-  nr=nrow(table_percent)
-  if (nr>4){
-    table_percent[5:nrow(table_percent),][["labels"]]=""
-  } 
-  # min_labels=min(5,nrow(table_percent))
-  # if (sum(!table_percent$labels<20)<min_labels){
-  #   nr=nrow(table_percent)
-  #   if ((min_labels+1)<nr){
-  #     table_percent[(min_labels+1):nrow(table_percent),][["labels"]]=""
-  #   }
-  # }else{
-  #   if (sum(table_percent$labels<20)>0){
-  #     table_percent[table_percent$labels<20,][["labels"]]=""
-  #   }
-  # }
-  table_percent[table_percent$labels!="",]$labels=paste(table_percent[table_percent$labels!="",]$DA,table_percent[table_percent$labels!="",]$labels)
-  table_percent$labels=lapply(table_percent$labels,add_perc_sign)
-  table_percent[table_percent$labels!="",]$labels=paste0(table_percent[table_percent$labels!="",]$labels,"(",table_percent[table_percent$labels!="",]$counts,")")
-  return(table_percent)
-}
-
-
-args = commandArgs(trailingOnly=TRUE)
-args[1] = "mergedquant.filtered.tsv"
-d=read_data_table(args[1])
-samplelist=d$samplelist
-circRNAlist=d$circRNAlist
-d=d$table
-
-for(i in 1:length(circRNAlist)) {        
-  cname=circRNAlist[[i]][1]
-  for (j in 1:length(samplelist)){
-    sname=samplelist[[j]][1]
-    df=filter_table_by_sname(filter_table_by_cname(d,cname),sname)
-    if(nrow(df)>0){
-      df=create_perc_table(df)
-      fname=paste0(cname,"-",sname,".png")
-      # print(fname)
-      png(fname)
-      # print(ggplot(df, aes(x = "", y = perc, fill = DA)) +
-      #   geom_bar(width = 1,stat = "identity") +
-      #   geom_label_repel(aes(label = labels, y = y_text)) +
-      #   scale_fill_manual(values=sample(col_vector,100,replace=TRUE))+
-      #   coord_polar(theta = "y", start = 0) +
-      #   theme_light()+
-      #   theme(legend.position="none")+
-      #   labs(x = "", y = "", title = paste(cname,sname,sep="-")))
-      pie(df$perc,labels = df$labels,main= paste0(cname,"-",sname))
-      dev.off()
-    }
-  }
-}
-
diff --git a/workflow/scripts/run_wrapper.bash b/workflow/scripts/run_wrapper.bash
deleted file mode 100644
index 155e223..0000000
--- a/workflow/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 "$@"
-
-
-
-
-