diff --git a/Dockerfile b/Dockerfile
index f682917..b5069a3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -58,19 +58,6 @@ RUN cargo install --locked maturin
 #install numpy
 RUN pip3 install numpy
 
-#pgr-tk installation
-RUN wget https://github.com/GeneDx/pgr-tk/releases/download/v0.5.1/pgr-tk-v0.5.1.zip \
-	&& unzip pgr-tk-v0.5.1.zip \
-	&& rm pgr-tk-v0.5.1.zip \
-	&& chmod +x release/* \
-	&& chmod +x wheels/* \
-	&& pip3 install wheels/pgrtk-0.5.1-cp310-cp310-linux_x86_64.whl
-
-ENV PATH /opt/release:$PATH
-
-#install wheels
-
-
 #ln python to python3 -not used right now but, who knows?
 RUN ln -s /usr/bin/python3 /usr/bin/python
 
diff --git a/cosigt.go b/cosigt.go
index f6c22b0..a62efcd 100644
--- a/cosigt.go
+++ b/cosigt.go
@@ -11,35 +11,18 @@ import (
 	"sort"
 	"strconv"
 	"strings"
+	"path"
 
+	"github.com/akamensky/argparse"
 	"gonum.org/v1/gonum/stat/combin"
 )
 
-//all these functions assume no errors in input files
 
-func GetCosineSimilarity(A []float64, B []float64) float64 {
-
-	var eucl_magn, dot_product, similarity float64
-
-	eucl_magn = GetMagnitude(A, B)
-
-	if eucl_magn > 0 {
-
-		dot_product = GetDotProduct(A, B)
-		similarity = dot_product / eucl_magn
-
-	} else {
-
-		similarity = 0
-
-	}
-
-	return similarity
-}
 
 func GetMagnitude(A []float64, B []float64) float64 {
 
 	var A_len, B_len float64
+
 	A_len = 0
 	B_len = 0
 
@@ -66,9 +49,42 @@ func GetDotProduct(A []float64, B []float64) float64 {
 	return dot_product
 }
 
+
+func GetCosineSimilarity(A []float64, B []float64) float64 {
+
+	/*
+	Simple calculation of cosine similarity
+	*/
+
+
+	var eucl_magn, dot_product, similarity float64
+
+	eucl_magn = GetMagnitude(A, B)
+
+	if eucl_magn > 0 {
+
+		dot_product = GetDotProduct(A, B)
+		similarity = dot_product / eucl_magn
+
+	} else {
+
+		similarity = 0
+
+	}
+
+	return similarity
+}
+
+
+
 func ReadBlacklist(s string) []string {
 
-	ids := make([]string, 0, 10) //don't want to re-allocate too many times
+	/*
+	Samples we may want to exclude, one-per-line
+	*/
+
+
+	ids := make([]string, 0, 100)
 
 	f, _ := os.Open(s)
 	defer f.Close()
@@ -87,6 +103,10 @@ func ReadBlacklist(s string) []string {
 
 func ReadGz(s string) ([]string, [][]float64) {
 
+	/*
+	Read the gzip-compressed files
+	*/
+
 	cov := make([][]float64, 0, 1000)
 	id := make([]string, 0, 1000)
 
@@ -124,6 +144,7 @@ func ReadGz(s string) ([]string, [][]float64) {
 		id = append(id, rec[0])
 
 	}
+
 	return id, cov
 }
 
@@ -176,22 +197,39 @@ func SumSlices(a []float64, b []float64) []float64 {
 
 func main() {
 
-	//I/O files
+	/*
+	Parsing of arguments with argparse
+	*/
+
+	parser := argparse.NewParser("cosigt", "genotyping loci in pangenome graphs using cosine distance")
+
+	p := parser.String("p", "paths", &argparse.Options{Required: true, Help: "gzip-compressed tsv file with path names and node coverages from odgi paths"})
+	g := parser.String("g", "gaf", &argparse.Options{Required: true, Help: "gzip-compressed gaf (graph alignment format) file for a sample from gafpack"})
+	b := parser.String("b", "blacklist", &argparse.Options{Required: false, Help: "txt file with names of paths to exclude (one per line)"})
+	o := parser.String("o", "output", &argparse.Options{Required: true, Help: "folder prefix for output files"})
+
+	err := parser.Parse(os.Args)
+
+	if err != nil  {
+
+		fmt.Print(parser.Usage(err))
+		os.Exit(1)
+
+	}
 
 	//read first table
-	hapid, gcov := ReadGz(os.Args[1])
+	hapid, gcov := ReadGz(*p)
 	//read second table
-	smpl, bcov := ReadGz(os.Args[2])
+	smpl, bcov := ReadGz(*g)
 	//read blacklist - it can be empty or not
-	blck := ReadBlacklist(os.Args[3])
-	//trace combinations we already use
+	blck := ReadBlacklist(*b)
+	//trace combinations we have already seen
 	seen:=make(map[int]bool)
-
 	//store results in map
 	m := make(map[string]float64)
-
+	//generate all possible diploid combination
 	n := len(hapid)
-	k := 2
+	k := 2 //fixed ploidy - this can be however adjusted
 	gen := combin.NewCombinationGenerator(n, k)
 
 	for gen.Next() {
@@ -204,8 +242,6 @@ func main() {
 			indiv := (hapid[h1] + "-" + hapid[h2])
 			m[indiv] = GetCosineSimilarity(sum, bcov[0])
 
-			//comment the following if we don't need to add homo
-
 			_,ok:=seen[h1]
 
 			if !ok {
@@ -228,7 +264,6 @@ func main() {
 
 			}
 
-			//comment above if we don't need to add homo
 
 		}
 
@@ -250,12 +285,19 @@ func main() {
 	})
 
 	//write combinations
-	_ = os.Mkdir(os.Args[4], os.ModePerm)
-	WriteMap(m, os.Args[4]+"/combos.tsv")
+	outpath:=path.Clean(*o)
+	_ = os.Mkdir(outpath, os.ModePerm)
+
+	combos:=path.Clean(outpath + "/combos.tsv")
+	WriteMap(m, combos)
 
 	//write best score
-	f, _ := os.Create(os.Args[4] + "/best_genotype.tsv")
+	best:=path.Clean(outpath + "/best_genotype.tsv")
+	f, _ := os.Create(best)
 	defer f.Close()
 	result := fmt.Sprintf("#sample\tbest_genotype\tbest_score\n%s\t%s\t%.16f\n", smpl[0], keys[0], m[keys[0]])
-	_, _ = f.WriteString(result)
+	_, _ = f.WriteString(result)	
+
+	//all done
+
 }
diff --git a/cosigt_smk/config/slurm/config.yaml b/cosigt_smk/config/slurm/config.yaml
index c04c6bf..0fac503 100644
--- a/cosigt_smk/config/slurm/config.yaml
+++ b/cosigt_smk/config/slurm/config.yaml
@@ -11,13 +11,13 @@ cluster:
 default-resources:
   - partition=cpuq
   - mem_mb=1000
-  - time="00:10:00"
+  - time=10
   - gpu=0
 max-jobs-per-second: 10
 max-status-checks-per-second: 20
 local-cores: 1
 latency-wait: 90
-jobs: 600
+jobs: 100
 keep-going: True
 rerun-incomplete: True
 printshellcmds: True
@@ -26,3 +26,4 @@ use-conda: True
 use-singularity: True
 verbose: True
 reason: True
+retries: 4
diff --git a/cosigt_smk/logs/.gitignore b/cosigt_smk/logs/.gitignore
deleted file mode 100644
index e69de29..0000000
diff --git a/cosigt_smk/snakemake.run.sh b/cosigt_smk/snakemake.run.sh
new file mode 100644
index 0000000..81cd8f3
--- /dev/null
+++ b/cosigt_smk/snakemake.run.sh
@@ -0,0 +1 @@
+snakemake --profile config/slurm --singularity-args "-B /group/soranzo/davide.bolognini/working/crams,/group/soranzo/davide.bolognini/working/graph,/ssu/gassu/reference_data/human_genomes/GRCh38,/localscratch" cosigt 
diff --git a/cosigt_smk/workflow/Snakefile b/cosigt_smk/workflow/Snakefile
index f6d37e4..d49f60b 100644
--- a/cosigt_smk/workflow/Snakefile
+++ b/cosigt_smk/workflow/Snakefile
@@ -7,21 +7,14 @@ df=(pd.read_table(config['samples'], dtype={'sample_id': str, 'cram':str})
 	.sort_index()
 )
 
-include: 'rules/pgrtk.smk'
-include: 'rules/pggb.smk'
 include: 'rules/extract.smk'
+include: 'rules/pggb.smk'
 include: 'rules/odgi.smk'
 include: 'rules/bwa-mem2.smk'
 include: 'rules/gfainject.smk'
 include: 'rules/gafpack.smk'
 include: 'rules/cosigt.smk'
-include: 'rules/evaluate.smk'
 
 rule cosigt:
 	input:
-		expand('results/cosigt/{sample}/{region}/best_genotype.tsv', sample=df['sample_id'].tolist(), region=config['region']),
-
-rule evaluation:
-	input:
-		expand('results/cosigt/evaluation/{region}/evaluation.pdf', region=config['region']),
-		expand('results/cosigt/evaluation/{region}/evaluation.jaccard.pdf', region=config['region'])
\ No newline at end of file
+		expand('results/cosigt/{sample}/{region}/best_genotype.tsv', sample=df['sample_id'].tolist(), region=config['region'])
diff --git a/cosigt_smk/workflow/rules/bwa-mem2.smk b/cosigt_smk/workflow/rules/bwa-mem2.smk
index d0c697d..6ec9e79 100644
--- a/cosigt_smk/workflow/rules/bwa-mem2.smk
+++ b/cosigt_smk/workflow/rules/bwa-mem2.smk
@@ -3,9 +3,9 @@ rule bwa_mem2_index:
 	bwa index
 	'''
 	input:
-		rules.pgrtk_filter.output
+		rules.odgi_paths_fasta.output
 	output:
-		multiext('results/pgrtk/fasta/{region}.fa', '.bwt.2bit.64', '.pac', '.ann', '.amb', '.0123')	
+		multiext('results/odgi/paths/fasta/{region}.fa', '.bwt.2bit.64', '.pac', '.ann', '.amb', '.0123')	
 	threads:
 		1
 	resources:
@@ -23,7 +23,7 @@ rule bwa_mem2_samtools_sort:
 	bwa-mem2 and sam-to-bam conversion with samtools
 	'''
 	input:
-		ref=rules.pgrtk_filter.output,
+		ref=rules.odgi_paths_fasta.output,
 		idx=rules.bwa_mem2_index.output,
 		sample=rules.samtools_fasta.output
 	output:
diff --git a/cosigt_smk/workflow/rules/cosigt.smk b/cosigt_smk/workflow/rules/cosigt.smk
index 4b14cf7..170a1d3 100644
--- a/cosigt_smk/workflow/rules/cosigt.smk
+++ b/cosigt_smk/workflow/rules/cosigt.smk
@@ -16,6 +16,6 @@ rule cosigt_genotype:
 		prefix='results/cosigt/{sample}/{region}'
 	shell:
 		'''
-		cosigt {input.zpath} {input.xpack} resources/extra/bad_samples.txt {params.prefix}
+		cosigt -p {input.zpath} -g {input.xpack} -b resources/extra/blacklist.txt -o {params.prefix}
 		'''
 
diff --git a/cosigt_smk/workflow/rules/extract.smk b/cosigt_smk/workflow/rules/extract.smk
index 26c81c8..9c7bada 100644
--- a/cosigt_smk/workflow/rules/extract.smk
+++ b/cosigt_smk/workflow/rules/extract.smk
@@ -1,4 +1,93 @@
 from glob import glob
+import os
+
+rule odgi_build:
+	'''
+	odgi build
+	'''
+	input:
+		config['graph']
+	output:
+		'results/odgi/build/' + os.path.basename(config['graph'].replace('.gfa', '.og'))
+	threads:
+		config['odgi']['threads']
+	resources:
+		mem_mb=lambda wildcards, attempt: attempt * config['odgi']['mem_mb'],
+		time=lambda wildcards, attempt: attempt * config['odgi']['time']
+	container:
+		'docker://pangenome/odgi:1707818641'
+	shell:
+		'''
+		odgi build \
+		-g {input} \
+		-o {output} \
+		-O \
+		-t {threads}
+		'''	
+
+rule odgi_extract:
+	'''
+	odgi extract
+	'''
+	input:
+		graph=rules.odgi_build.output,
+		region=lambda wildcards: glob('resources/regions/{region}.bed'.format(region=wildcards.region))
+	output:
+		'results/odgi/extract/{region}.og'
+	threads:
+		config['odgi']['threads']
+	resources:
+		mem_mb=lambda wildcards, attempt: attempt * config['odgi']['mem_mb'],
+		time=lambda wildcards, attempt: attempt * config['odgi']['time']
+	container:
+		'docker://pangenome/odgi:1707818641'
+	shell:
+		'''
+		odgi extract \
+		-i {input.graph} \
+		-b {input.region} \
+		-t {threads} \
+		-O \
+		-o {output}
+		'''
+
+
+rule odgi_paths_fasta:
+	'''
+	odgi paths
+	'''
+	input:
+		rules.odgi_extract.output
+	output:
+		'results/odgi/paths/fasta/{region}.fa'
+	threads:
+		1
+	container:
+		'docker://pangenome/odgi:1707818641'
+	shell:
+		'''
+		odgi paths \
+		-i {input} \
+		-f > {output}
+		'''
+
+rule faidx:
+	'''
+	samtools faidx
+	'''
+	input:
+		rules.odgi_paths_fasta.output
+	output:
+		'results/odgi/paths/fasta/{region}.fa.fai'
+	threads:
+		1
+	container:
+		'docker://davidebolo1993/graph_genotyper:latest'
+	shell:
+		'''
+		samtools faidx {input}
+		'''
+
 
 rule get_proper_region:
 	input:
@@ -11,7 +100,7 @@ rule get_proper_region:
 		path=config['path']
 	shell:
 		'''
-		grep {params.path} {input} | cut -f 1 | cut -d "_" -f 1,3-4 | tr '_' '\t' > {output}
+		grep {params.path} {input} | cut -f 1 | cut -d "#" -f 2 | tr ':' '\t'| tr '-' '\t' > {output}
 		'''
 	
 rule samtools_view:
@@ -31,8 +120,8 @@ rule samtools_view:
 		ref=config['reference'],
 		region='{region}'
 	resources:
-		mem_mb=config['samtools']['mem_mb'],
-		time=config['samtools']['time']
+		mem_mb=lambda wildcards, attempt: attempt * config['samtools']['mem_mb'],
+		time=lambda wildcards, attempt: attempt * config['samtools']['time']
 	shell:
 		'''
 		samtools view \
@@ -42,7 +131,7 @@ rule samtools_view:
 		-@ {threads} \
 		-L {input.bed} \
 		-M \
-		{input.sample} \
+		{input.sample}
 		'''
 
 rule samtools_fasta:
@@ -58,8 +147,8 @@ rule samtools_fasta:
 	container:
 		'docker://davidebolo1993/graph_genotyper:latest'
 	resources:
-		mem_mb=config['samtools']['mem_mb'],
-		time=config['samtools']['time']
+		mem_mb=lambda wildcards, attempt: attempt * config['samtools']['mem_mb'],
+		time=lambda wildcards, attempt: attempt * config['samtools']['time']
 	shell:
 		'''
 		samtools fasta \
diff --git a/cosigt_smk/workflow/rules/odgi.smk b/cosigt_smk/workflow/rules/odgi.smk
index 17331e7..4224e01 100644
--- a/cosigt_smk/workflow/rules/odgi.smk
+++ b/cosigt_smk/workflow/rules/odgi.smk
@@ -1,5 +1,3 @@
-import os
-
 rule odgi_chop:
 	'''
 	odgi chop
@@ -11,7 +9,7 @@ rule odgi_chop:
 	threads:
 		1
 	container:
-		'docker://pangenome/odgi:1689324294'
+		'docker://pangenome/odgi:1707818641'
 	shell:
 		'''
 		odgi chop  \
@@ -31,7 +29,7 @@ rule odgi_view:
 	threads:
 		1
 	container:
-		'docker://pangenome/odgi:1689324294'
+		'docker://pangenome/odgi:1707818641'
 	shell:
 		'''
 		odgi view \
@@ -50,7 +48,7 @@ rule odgi_paths_matrix:
 	threads:
 		1
 	container:
-		'docker://pangenome/odgi:1689324294'
+		'docker://pangenome/odgi:1707818641'
 	shell:
 		'''
 		odgi paths \
@@ -69,7 +67,7 @@ rule odgi_similarity:
 	threads:
 		1
 	container:
-		'docker://pangenome/odgi:1689324294'
+		'docker://pangenome/odgi:1707818641'
 	shell:
 		'''
 		odgi similarity \
diff --git a/cosigt_smk/workflow/rules/pggb.smk b/cosigt_smk/workflow/rules/pggb.smk
index be6265b..cd9d2d2 100644
--- a/cosigt_smk/workflow/rules/pggb.smk
+++ b/cosigt_smk/workflow/rules/pggb.smk
@@ -3,7 +3,7 @@ rule pggb:
 	pggb
 	'''
 	input:
-		fasta=rules.pgrtk_filter.output,
+		fasta=rules.odgi_paths_fasta.output,
 		index=rules.faidx.output
 	output:
 		'results/pggb/{region}.og'
@@ -12,8 +12,8 @@ rule pggb:
 	container:
 		'docker://pangenome/pggb:latest'
 	resources:
-		mem_mb=config['pggb']['mem_mb'],
-		time=config['pggb']['time']
+		mem_mb=lambda wildcards, attempt: attempt * config['pggb']['mem_mb'],
+		time=lambda wildcards, attempt: attempt * config['pggb']['time']
 	params:
 		prefix='results/pggb/{region}'
 	shell:
@@ -22,11 +22,7 @@ rule pggb:
 			-i {input.fasta} \
 			-o {params.prefix} \
 			-t {threads} \
-			-n 200 \
-			-S \
-			-A \
-			-p 90 \
-			-s 5k \
-			-k 419 \
+			-n 94 \
+			-c 2 \
 		&& mv {params.prefix}/*smooth.final.og {output}
 		'''
diff --git a/cosigt_smk/workflow/rules/pgrtk.smk b/cosigt_smk/workflow/rules/pgrtk.smk
deleted file mode 100644
index 491fc08..0000000
--- a/cosigt_smk/workflow/rules/pgrtk.smk
+++ /dev/null
@@ -1,105 +0,0 @@
-#rule pgrtk_get_seq:
-#	'''
-#	run pgrtk api - deprecating in favour of cli, but keeping this here just in case want to re-introduce at some point
-#	'''
-#	input:
-#		agc=config['agc'],
-#		region=lambda wildcards: glob('resources/regions/{region}.bed'.format(region=wildcards.region))
-#	output:
-#		'results/pgrtk/{region}.fa'
-#	threads:
-#		config['pgrtk']['threads']
-#	container:
-#		'docker://davidebolo1993/graph_genotyper:latest'
-#	params:
-#		padding=config['pgrtk']['padding']
-#	resources:
-#		mem_mb=config['pgrtk']['mem_mb'],
-#		time=config['pgrtk']['time']
-#	shell:
-#		'''
-#		python workflow/scripts/pypgrtk.py {input.agc} {input.region} {params.padding} {output}
-#		'''
-
-rule pgrtk_fetch_seqs:
-	'''
-	run pgrtk fetch
-	'''
-	input:
-		agc=config['agc'],
-		region=lambda wildcards: glob('resources/regions/{region}.bed'.format(region=wildcards.region))
-	output:
-		'results/pgrtk/fetch/{region}.fa'
-	threads:
-		32
-	container:
-		'docker://davidebolo1993/graph_genotyper:latest'
-	resources:
-		mem_mb=config['pgrtk']['mem_mb'],
-		time=config['pgrtk']['time']
-	params:
-		agc_prefix=config['agc'].replace('.agc','')
-	shell:
-		'''
-		pgr-fetch-seqs {params.agc_prefix} -r {input.region} > {output}
-		'''
-
-rule pgrtk_query:
-	'''
-	run pgrtk query
-	'''
-	input:
-		agc=config['agc'],
-		fasta=rules.pgrtk_fetch_seqs.output
-	output:
-		hit='results/pgrtk/query/{region}.000.hit',
-		fasta='results/pgrtk/query/{region}.000.fa'
-	threads:
-		32
-	container:
-		'docker://davidebolo1993/graph_genotyper:latest'
-	resources:
-		mem_mb=config['pgrtk']['mem_mb'],
-		time=config['pgrtk']['time']
-	params:
-		prefix='results/pgrtk/query/{region}',
-		agc_prefix=config['agc'].replace('.agc','')
-	shell:
-		'''
-		pgr-query {params.agc_prefix} {input.fasta} {params.prefix}
-		'''
-
-rule pgrtk_filter:
-	'''
-	filter hits
-	'''
-	input:
-		hit=rules.pgrtk_query.output.hit,
-		fasta=rules.pgrtk_query.output.fasta
-	output:
-		'results/pgrtk/fasta/{region}.fa'
-	threads:
-		1
-	conda:
-		'../envs/python.yml'
-	shell:
-		'''
-		python workflow/scripts/filter_pgrtk.py {input.fasta} {input.hit} {output}
-		'''
-
-rule faidx:
-	'''
-	samtools faidx
-	'''
-	input:
-		rules.pgrtk_filter.output
-	output:
-		'results/pgrtk/fasta/{region}.fa.fai'
-	threads:
-		1
-	container:
-		'docker://davidebolo1993/graph_genotyper:latest'
-	shell:
-		'''
-		samtools faidx {input}
-		'''
\ No newline at end of file
diff --git a/cosigt_smk/workflow/rules/evaluate.smk b/cosigt_smk/workflow/scripts/evaluate.smk
similarity index 100%
rename from cosigt_smk/workflow/rules/evaluate.smk
rename to cosigt_smk/workflow/scripts/evaluate.smk
diff --git a/cosigt_smk/workflow/scripts/filter_pgrtk.py b/cosigt_smk/workflow/scripts/filter_pgrtk.py
deleted file mode 100644
index b19bbf1..0000000
--- a/cosigt_smk/workflow/scripts/filter_pgrtk.py
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/python3 env
-
-#standard libraries
-import os
-import sys
-import pyfaidx
-
-def main(input_fa,input_hit,output_fa):
-
-    fasta=pyfaidx.Fasta(input_fa)
-
-    with open(input_hit) as fin, open(output_fa, 'w') as fout:
-        
-        for row in fin:
-            
-            row = row.strip().split("\t")
-            
-            if row[0][0] == "#":
-                
-                continue
-            
-            (q_idx, q_name, query_bgn, query_end, q_len, aln_anchor_count, 
-            src, ctg, ctg_bgn, ctg_end, orientation, out_seq_name) = row
-            query_bgn = int(query_bgn)
-            query_end = int(query_end)
-            ctg_bgn = int(ctg_bgn)
-            ctg_end = int(ctg_end)
-            q_len = int(q_len)
-            
-            #maybe need to check why this is 12000 - but itworks for test regions
-            if query_bgn > 12000 or q_len - query_end > 12000:
-            
-                continue
-            
-            if abs(ctg_end-ctg_bgn) > q_len * 3:
-            
-                continue
-            
-            key=[x for x in fasta.keys() if ctg+ '_' + str(ctg_bgn) in x]
-            seq=fasta[key[0]][:].seq
-            fout.write('>' + key[0].split('::')[1] + '\n' + seq + '\n')
-
-
-if __name__ == '__main__':
-
-    input_fa=os.path.abspath(sys.argv[1])
-    input_hit=os.path.abspath(sys.argv[2])
-    output_fa=os.path.abspath(sys.argv[3])
-    main(input_fa,input_hit,output_fa)
\ No newline at end of file
diff --git a/cosigt_smk/workflow/scripts/organize.py b/cosigt_smk/workflow/scripts/organize.py
index 4770221..aa307e5 100644
--- a/cosigt_smk/workflow/scripts/organize.py
+++ b/cosigt_smk/workflow/scripts/organize.py
@@ -1,12 +1,9 @@
 #!/usr/bin/python3 env
 
 #standard libraries
-
 import os
-import sys
 import glob
 import yaml
-import shutil
 import argparse
 from argparse import HelpFormatter
 
@@ -65,37 +62,37 @@ def default_parameters(args):
 	d['bwa-mem2']=dict()
 	d['bwa-mem2']['threads'] = args.aln_threads
 	d['bwa-mem2']['mem_mb'] = args.aln_memory
-	d['bwa-mem2']['time'] = double_quote(args.aln_time)
+	d['bwa-mem2']['time'] = args.aln_time
 
 	#bwa-mem
 	d['bwa']=dict()
 	d['bwa']['threads'] = args.aln_threads
 	d['bwa']['mem_mb'] = args.aln_memory
-	d['bwa']['time'] = double_quote(args.aln_time)
+	d['bwa']['time'] =  args.aln_time
 
 	#minimap2
 	d['minimap2']=dict()
 	d['minimap2']['threads'] = args.aln_threads
 	d['minimap2']['mem_mb'] = args.aln_memory
-	d['minimap2']['time'] = double_quote(args.aln_time)
+	d['minimap2']['time'] =  args.aln_time
 
 	#samtools
 	d['samtools']=dict()
 	d['samtools']['threads'] = args.sam_threads
 	d['samtools']['mem_mb'] = args.sam_memory
-	d['samtools']['time'] =  double_quote(args.sam_time)
+	d['samtools']['time'] =   args.sam_time
 
-	#pgrtk
-	d['pgrtk']=dict()
-	#d['pgrtk']['padding'] = args.pgrtk_padding
-	d['pgrtk']['mem_mb'] = args.pgrtk_memory
-	d['pgrtk']['time'] =  double_quote(args.pgrtk_time)
+	#odgi
+	d['odgi']=dict()
+	d['odgi']['threads'] = args.odgi_threads
+	d['odgi']['mem_mb'] = args.odgi_memory
+	d['odgi']['time'] =  args.odgi_time
 
 	#pggb
 	d['pggb']=dict()
 	d['pggb']['threads'] = args.pggb_threads
 	d['pggb']['mem_mb'] = args.pggb_memory
-	d['pggb']['time'] =  double_quote(args.pggb_time)
+	d['pggb']['time'] =  args.pggb_time
 
 	return d
 
@@ -106,41 +103,41 @@ def main():
 	parse arguments and organize inputs for running cosigt properly without additional efforts from the users
 	'''
 
-	parser = argparse.ArgumentParser(prog='cosigt', description='''COsine SImilarity-based GenoTyper''', epilog='''This program was developed by Davide Bolognini at Human Technopole.''', formatter_class=CustomFormat) 
+	parser = argparse.ArgumentParser(prog='cosigt', description='''COsine SImilarity-based GenoTyper''', epilog='''Developed by Davide Bolognini @ Human Technopole''', formatter_class=CustomFormat) 
 
 	required = parser.add_argument_group('Required I/O arguments')
 
 	required.add_argument('-r','--reference', help='reference genome in FASTA format', metavar='FASTA', required=True)
-	required.add_argument('--agc', help='agc file from pgrtk - available at https://giab-data.s3.amazonaws.com/PGR-TK-Files/pgr-tk-HGRP-y1-evaluation-set-v0.tar', metavar='AGC', required=True)
+	required.add_argument('--gfa', help='variation graph in .gfa format', metavar='GFA', required=True)
 	required.add_argument('-a', '--alignment', help='folder with alignment files (bam,cram) - and their index - to use', metavar='FOLDER', required=True)
 	required.add_argument('--roi', help='one or more regions of interest in BED format', metavar='BED', required=True)
 
 	additional = parser.add_argument_group('Additional I/O arguments')
-
 	additional.add_argument('--blacklist', help='blacklist of samples (one per line) that should not be included in the analysis [None]', metavar='', required=False, default=None)
-	additional.add_argument('--path', help='path name in the graph to use as a reference [hg38]',type=str, default='hg38')
+	additional.add_argument('--path', help='path name in the pangenome graph to be used as a reference [grch38]',type=str, default='grch38')
+	additional.add_argument('--binds', help='additional paths to bind for singularity in /path/1,/path/2 format', type=str, default='/localscratch')
 
 	metrics = parser.add_argument_group('Specify #threads, memory and time requirements')
 
 	#alignment
 	metrics.add_argument('--aln_threads', help='threads - aligner [5]',type=int, default=5)
-	metrics.add_argument('--aln_time', help='max time (hh:mm:ss) - aligner ["00:02:30"]',type=str, default='00:02:30')
-	metrics.add_argument('--aln_memory', help='max memory (mb) - aligner[6000]',type=int, default=6000)
+	metrics.add_argument('--aln_time', help='max time (minutes) - aligner [2]',type=int, default=2)
+	metrics.add_argument('--aln_memory', help='max memory (mb) - aligner[5000]',type=int, default=5000)
 
 	#samtools extraction and sort
-	metrics.add_argument('--sam_threads', help='threads - samtools (view/sort) commands [1]',type=int, default=1)
-	metrics.add_argument('--sam_time', help='max time (hh:mm:ss) - samtools (view/sort) commands ["00:08:00"]',type=str, default='00:08:00')
+	metrics.add_argument('--sam_threads', help='threads - samtools (view/sort) commands [2]',type=int, default=2)
+	metrics.add_argument('--sam_time', help='max time (minutes) - samtools (view/sort) commands [8]',type=int, default=8)
 	metrics.add_argument('--sam_memory', help='max memory (mb) - samtools (view/sort) commands [1000]',type=int, default=1000)
 
-	#pgrtk
-	metrics.add_argument('--pgrtk_padding', help='padding - pgrtk commands [200000]',type=int, default=200000)
-	metrics.add_argument('--pgrtk_time', help='max time (hh:mm:ss) - pgrtk commands ["00:10:00"]',type=str, default='00:10:00')
-	metrics.add_argument('--pgrtk_memory', help='max memory (mb) - pgrtk commands [35000]',type=int, default=35000)
-
 	#pggb
-	metrics.add_argument('--pggb_threads', help='threads - pggb command [32]',type=int, default=32)
-	metrics.add_argument('--pggb_time', help='max time (hh:mm:ss) - pggb commands ["00:25:00"]',type=str, default='00:25:00')
-	metrics.add_argument('--pggb_memory', help='max memory (mb) - pggb commands [2000]',type=int, default=2000)
+	metrics.add_argument('--pggb_threads', help='threads - pggb command [24]',type=int, default=24)
+	metrics.add_argument('--pggb_time', help='max time (minutes) - pggb commands [35]',type=int, default=35)
+	metrics.add_argument('--pggb_memory', help='max memory (mb) - pggb commands [20000]',type=int, default=20000)
+
+	#odgi build and extract
+	metrics.add_argument('--odgi_threads', help='threads - odgi (build/extract) commands [10]',type=int, default=10)
+	metrics.add_argument('--odgi_time', help='max time (minutes) - odgi (build/extract) commands [10]',type=int, default=10)
+	metrics.add_argument('--odgi_memory', help='max memory (mb) - odgi (build/extract) commands [30000]',type=int, default=30000)
 
 	args = parser.parse_args()
 
@@ -162,13 +159,15 @@ def main():
 	out_resources=os.path.join(wd,'resources')
 	out_aln=os.path.join(out_resources, 'alignment')
 	os.makedirs(out_aln, exist_ok=True)
-	out_agc=os.path.join(out_resources, 'agc')
-	os.makedirs(out_agc, exist_ok=True)
+	#out_agc=os.path.join(out_resources, 'agc')
+	#os.makedirs(out_agc, exist_ok=True)
+	out_gfa=os.path.join(out_resources, 'graph')
+	os.makedirs(out_gfa, exist_ok=True)
 	out_ref=os.path.join(out_resources, 'reference')
 	os.makedirs(out_ref, exist_ok=True)
 	out_extra=os.path.join(out_resources, 'extra')
 	os.makedirs(out_extra,exist_ok=True)
-	blcklst_out=os.path.join(out_extra, 'bad_samples.txt')
+	blcklst_out=os.path.join(out_extra, 'blacklist.txt')
 	out_regions=os.path.join(out_resources, 'regions')
 	os.makedirs(out_regions,exist_ok=True)
 
@@ -176,7 +175,6 @@ def main():
 	out_sing=os.path.join(wd, 'singularity_bind_paths.csv')
 
 	#blacklist of samples to exclude
-
 	blcklst=[]
 
 	if args.blacklist is not None:
@@ -190,9 +188,7 @@ def main():
 		
 	else:
 
-		with open(blcklst_out, 'w') as bad_samples_out:
-
-			pass
+		open(blcklst_out, 'w').close()
 
 	#symlink alignments
 	alns=sorted(glob.glob(args.alignment+'/*am*'))
@@ -220,33 +216,26 @@ def main():
 
 			if aln.endswith('am'): #this is not an index, rather a true alignment
 
-				sample_name=bnaln.split('.')[0]
+				sample_name='.'.join(bnaln.split('.')[:-1])
 				samples_out.write(sample_name + '\t' + out_aln_file + '\n')
 
 	#add to config
 	d['samples'] = out_samples
 
-	#symlink agc
-	agc=os.path.abspath(args.agc)
-	agc_dir=os.path.dirname(agc)
-	agc_file=os.path.basename(agc)
-	agc_pattern=agc_file.replace('.agc', '')
-	agc_files=glob.glob(agc_dir + '/' +agc_pattern+'*')
-
-	for f in agc_files:
-
-		try:
-
-			os.symlink(f, os.path.join(out_agc, os.path.basename(f)))
+	#symlink gfa
+	out_gfa_file=os.path.join(out_gfa, os.path.basename(args.gfa))
 
-		except:
+	try:
 
-			pass
+		os.symlink(os.path.abspath(args.gfa), out_gfa_file)
+	
+	except:
 
-	out_agc_file=os.path.join(out_agc,agc_file)
+		pass
 
 	#add to config
-	d['agc'] = out_agc_file
+	d['graph'] = out_gfa_file
+
 
 	#symlink reference
 	out_reference_file=os.path.join(out_ref, os.path.basename(args.reference))
@@ -266,13 +255,13 @@ def main():
 	#add to config
 	d['region'] = list()
 
-
 	with open(args.roi) as bed_in:
 
 		for line in bed_in:
 
 			l=line.rstrip().split('\t')
-			region=l[0] + '_' + str(int(l[1])-args.pgrtk_padding) + '_' + str(int(l[2])+args.pgrtk_padding)
+						
+			region=l[0] + '_' + l[1] + '_' + l[2]
 
 			#put regions in the config fille
 			d['region'].append(region)
@@ -282,7 +271,7 @@ def main():
 
 			with open(region_out, 'w') as out_region:
 
-				out_region.write(region + '\t' + args.path +'_tagged.fa' + '\t' + l[0] + '_' + args.path + '\t' + str(int(l[1])-args.pgrtk_padding) + '\t' + str(int(l[2])+args.pgrtk_padding) + '\t0\n')
+				out_region.write(args.path +'#'+ l[0] + '\t' + l[1] + '\t' + l[2] + '\t' + region+'\n')
 
 	
 	#dump config
@@ -291,7 +280,6 @@ def main():
 	yml_out.close()
 
 	#remove single quotes
-
 	with open(out_yaml_tmp) as filein, open(out_yaml, 'w') as fileout:
 
 		for line in filein:
@@ -301,10 +289,13 @@ def main():
 
 	os.remove(out_yaml_tmp)
 
-	#write singularity paths for those using singularity
-	with open(out_sing, 'w') as singpath:
+	#write command
+	singpath=','.join([os.path.abspath(args.alignment),os.path.dirname(os.path.abspath(args.gfa)),os.path.dirname(os.path.abspath(args.reference)),args.binds])
+	command_out=' '.join(['snakemake --profile config/slurm --singularity-args "-B '+ singpath + '" cosigt'])
+	
+	with open('snakemake.run.sh', 'w') as out:
 
-		singpath.write(','.join([os.path.abspath(args.alignment),os.path.dirname(os.path.abspath(args.agc)),os.path.dirname(os.path.abspath(args.reference)),'/localscratch']) + '\n')
+		out.write(command_out + '\n')
 
 
 if __name__ == '__main__':
diff --git a/cosigt_smk/workflow/scripts/pypgrtk.py b/cosigt_smk/workflow/scripts/pypgrtk.py
deleted file mode 100644
index d60c470..0000000
--- a/cosigt_smk/workflow/scripts/pypgrtk.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/python3
-
-import pgrtk
-import os
-import sys
-
-def main(agc_file,bed_file,padding,out_file):
-
-    #load agc_file
-    ref_db=pgrtk.AGCFile(agc_file)
-
-    #load region
-    with open(bed_file) as bed:
-
-        for line in bed:
-
-            fields=line.rstrip().split('\t')
-            ref_file_name, roi_chr, roi_b, roi_e = fields[0],fields[1], int(fields[2]), int(fields[3])
-            roi_len=roi_e - roi_b
-            break 
-            #not needed - but make sure we read just one line
-
-    #sdb
-    sdb = pgrtk.SeqIndexDB()
-    sdb.load_from_agc_index(agc_file.replace('.agc', ''))
-
-    #retrieve roi sequence
-    roi_seq = ref_db.get_sub_seq(ref_file_name, roi_chr, roi_b-padding, roi_e+padding)
-
-    #find hits in the pangenomic reference
-    aln_range = pgrtk.query_sdb(sdb, roi_seq, merge_range_tol=100000)
-    seq_list=[]
-
-    for k in list(aln_range.keys()):
-
-        ctg_name, source, _ = sdb.seq_info[k]
-        rgns = aln_range[k].copy()
-        rgns = pgrtk.merge_regions(rgns, tol=1000)
-
-        for rgn in rgns:
-
-            b, e,_, orientation, aln = rgn
-            print(ctg_name,b,e)
-
-            if aln[0][0][0] > padding or aln[-1][0][1] < padding + roi_len:
-
-                continue
-            
-            if e-b < 0.75 * (roi_len + 2 * padding):
-
-                continue
-
-            seq =  sdb.get_sub_seq(source, ctg_name, b, e)
-    
-            if orientation == 1:
-
-                seq = pgrtk.rc_byte_seq(seq)
-
-
-            seq_list.append(('{}_{}_{}_{}'.format(ctg_name, b, e, orientation), seq))
-
-    f0 = open(out_file, 'w')
-    
-    for ctg, seq in seq_list:
-            
-        print('>{}'.format(ctg), file=f0)
-        print(pgrtk.u8_to_string(seq), file=f0)
-            
-    f0.close()
-
-
-if __name__ == '__main__':
-
-    agc_file=os.path.abspath(sys.argv[1])
-    bed_file=os.path.abspath(sys.argv[2])
-    padding=int(sys.argv[3])
-    out_file=os.path.abspath(sys.argv[4])
-    print(agc_file,bed_file,padding,out_file)
-    main(agc_file,bed_file,padding,out_file)
-
-
-
-