Minor changes

Author: kjaisingh

src/svtk/svtk/standardize/std_dragen_cnv.py

@@ -21,17 +21,16 @@ def standardize_records(self):
         """
 
         # Iterate over records
-        n = 0
         for record in self.filter_raw_vcf():
-            # Skip records that are reference            
+            # Skip records that are reference
             if 'SVTYPE' not in record.info:
                 continue
 
             # Reset filters
             record.filter.clear()
-                
+
             yield self.standardize_record(record)
-    
+
     def standardize_info(self, std_rec, raw_rec):
         """
         Standardize Dragen CNV record.
@@ -69,7 +68,7 @@ def standardize_info(self, std_rec, raw_rec):
 
         # Define ALGORITHMS
         std_rec.info['ALGORITHMS'] = ['depth']
-        
+
         return std_rec
 
     def standardize_alts(self, std_rec, raw_rec):
@@ -90,22 +89,22 @@ def standardize_alts(self, std_rec, raw_rec):
         std_rec.stop = stop
 
         return std_rec
-    
+
     def standardize_format(self, std_rec, raw_rec):
         """
         Parse ./1 GTs for DUPs into 1/1.
         """
-            
+
         source = std_rec.info['ALGORITHMS'][0]
-        
+
         for sample, std_sample in zip(raw_rec.samples, self.std_sample_names):
             gt = raw_rec.samples[sample]['GT']
             if self.call_null_sites:
                 if gt == (None, None):
                     gt = (0, 1)
                 if gt == (None,):
                     gt = (1,)
-            
+
             if None in gt or any(allele == "." for allele in gt):
                 gt = (1, 1)
             std_rec.samples[std_sample]['GT'] = gt
@@ -116,5 +115,3 @@ def standardize_format(self, std_rec, raw_rec):
                 std_rec.samples[std_sample][source] = 0
 
         return std_rec
-    
-    

src/svtk/svtk/standardize/std_manta.py

@@ -80,7 +80,7 @@ def standardize_info(self, std_rec, raw_rec):
         if pos == 54564370:
             print(f"{std_rec.id}: {end}")
             print(f"{std_rec.id}: {std_rec.stop}")
-        
+
         # Strand parsing
         if svtype == 'INV':
             if 'INV3' in raw_rec.info.keys():

wdl/DefragmentCnvsVcf.wdl

@@ -4,7 +4,7 @@ workflow DefragmentCnvsVcf {
 	input {
 		File vcf              								# Input VCF
 		File vcf_idx          								# Input VCF index file
-		Float? max_dist        									# Maximum distance for merging CNVs
+		Float? max_dist        								# Maximum distance for merging CNVs
 		String prefix													# Prefix for output files
 
 		String sv_pipeline_docker							# Docker image path
@@ -14,6 +14,7 @@ workflow DefragmentCnvsVcf {
 		input:
 			vcf = vcf,
 			vcf_idx = vcf_idx,
+			prefix = prefix,
 			sv_pipeline_docker = sv_pipeline_docker
 	}
 
@@ -30,6 +31,7 @@ workflow DefragmentCnvsVcf {
 			vcf = vcf,
 			vcf_idx = vcf_idx,
 			bed = DefragmentCnvs.bed_out,
+			prefix = prefix,
 			sv_pipeline_docker = sv_pipeline_docker
 	}