fixing [ci skip]

cosigt_smk/workflow/rules/pggb.smk

@@ -3,7 +3,8 @@ rule pggb:
     pggb
     '''
 	input:
-		rules.pgrtk_get_seq.output,
+		fasta=rules.pgrtk_get_seq.output,
+		index=rules.faidx.output
 	output:
 		'results/pggb/{region}.og'
 	threads:
@@ -18,7 +19,7 @@ rule pggb:
 	shell:
 		'''
         pggb \
-            -i {input} \
+            -i {input.fasta} \
             -o {params.prefix} \
             -p 90 \
             -s 5k \

cosigt_smk/workflow/rules/pgrtk.smk

@@ -1,16 +1,39 @@
 rule pgrtk_get_seq:
+	'''
+	run pgrtk api
+	'''
 	input:
 		agc=config['agc'],
 		region=lambda wildcards: glob('resources/regions/{region}.bed'.format(region=wildcards.region))
 	output:
 		'results/pgrtk/{region}.fa'
 	threads:
-		1
+		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 faidx:
+	'''
+	samtools faidx
+	'''
+	input:
+		rules.pgrtk_get_seq.output
+	output:
+		'results/pgrtk/{region}.fa.fai'
+	threads:
+		1
+	container:
+		'docker://davidebolo1993/graph_genotyper:latest'
+	shell:
+		'''
+		samtools faidx {input}
 		'''

cosigt_smk/workflow/scripts/organize.py

@@ -88,6 +88,7 @@ def default_parameters(args):
 	#pgrtk
 	d['pgrtk']=dict()
 	d['pgrtk']['padding'] = args.pgrtk_padding
+	d['pgrtk']['threads'] = args.pgrtk_threads
 	d['pgrtk']['mem_mb'] = args.pgrtk_memory
 	d['pgrtk']['time'] =  double_quote(args.pgrtk_time)
 
@@ -134,12 +135,13 @@ def main():
 
 	#pgrtk
 	metrics.add_argument('--pgrtk_padding', help='padding (#bps) - pgrtk commands [100000]',type=int, default=100000)
+	metrics.add_argument('--pgrtk_threads', help='threads - pgrtk commands [10]',type=int, default=10)
 	metrics.add_argument('--pgrtk_time', help='max time (hh:mm:ss) - pgrtk commands ["00:05:00"]',type=str, default='00:05:00')
 	metrics.add_argument('--pgrtk_memory', help='max memory (mb) - samtools (view/sort) commands [30000]',type=int, default=30000)
 
 	#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) - odgi (build) commands ["00:15:00"]',type=str, default='00:15:00')
+	metrics.add_argument('--pggb_time', help='max time (hh:mm:ss) - odgi (build) commands ["00:25:00"]',type=str, default='00:25:00')
 	metrics.add_argument('--pggb_memory', help='max memory (mb) - odgi (build) commands [5000]',type=int, default=5000)
 
 	args = parser.parse_args()