From bf500c5814ce24d0b87591daed40b35ee1504bf1 Mon Sep 17 00:00:00 2001
From: nkumar2 <nkumar2@ebi.ac.uk>
Date: Wed, 4 Feb 2026 11:06:17 +0000
Subject: [PATCH] add property for duplicate SS acc QC in accessioning pipeline
 properties

---
 ebi_eva_internal_pyutils/spring_properties.py |  6 ++++--
 tests/internal/test_spring_prop.py            | 15 +++++++++------
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/ebi_eva_internal_pyutils/spring_properties.py b/ebi_eva_internal_pyutils/spring_properties.py
index e7c1c89..25db94c 100644
--- a/ebi_eva_internal_pyutils/spring_properties.py
+++ b/ebi_eva_internal_pyutils/spring_properties.py
@@ -134,7 +134,8 @@ def _common_accessioning_clustering_properties(self, *, assembly_accession, read
 
     def get_accessioning_properties(self, *, read_preference='primary', job_name=None, target_assembly=None, fasta=None,
                                     assembly_report=None, project_accession=None, aggregation='BASIC',
-                                    taxonomy_accession=None, vcf_file='', output_vcf='', chunk_size=100):
+                                    taxonomy_accession=None, vcf_file='', output_vcf='', duplicate_ss_acc_file='',
+                                    chunk_size=100):
         """Properties for accessioning pipeline."""
         return self._format(
             self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
@@ -150,7 +151,8 @@ def get_accessioning_properties(self, *, read_preference='primary', job_name=Non
                 'parameters.taxonomyAccession': taxonomy_accession,
                 'parameters.vcfAggregation': aggregation,
                 'parameters.vcf': vcf_file,
-                'parameters.outputVcf': output_vcf
+                'parameters.outputVcf': output_vcf,
+                'parameters.duplicateSSAccFile': duplicate_ss_acc_file
             },
         )
 
diff --git a/tests/internal/test_spring_prop.py b/tests/internal/test_spring_prop.py
index 53230df..0254210 100644
--- a/tests/internal/test_spring_prop.py
+++ b/tests/internal/test_spring_prop.py
@@ -165,7 +165,8 @@ def test_get_accessioning_properties(self):
 parameters.taxonomyAccession=9906
 parameters.vcfAggregation=BASIC
 parameters.vcf=/path/to/vcf_file.vcf
-parameters.outputVcf=
+parameters.outputVcf=/path/to/output_vcf.vcf
+parameters.duplicateSSAccFile=/path/to/duplicate_ss_acc_file.vcf
 
 accessioning.submitted.categoryId=ss
 accessioning.clustered.categoryId=rs
@@ -181,7 +182,8 @@ def test_get_accessioning_properties(self):
         assert self.prop.get_accessioning_properties(
             job_name='SUBSNP_ACCESSION_JOB', target_assembly='GCA_00000001.1', fasta='/path/to/fasta.fa',
             assembly_report='/path/to/assembly_report.txt', project_accession='PRJEB0001', aggregation='BASIC',
-            taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf') == expected
+            taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf', output_vcf='/path/to/output_vcf.vcf',
+            duplicate_ss_acc_file='/path/to/duplicate_ss_acc_file.vcf') == expected
 
     def test_get_variant_load_properties(self):
         expected = '''spring.data.mongodb.uri=mongodb://mongouser:mongop%40ssword@mongos-host1.example.com:27017,mongos-host2.example.com:27017/?retryWrites=true&authSource=admin
@@ -383,7 +385,8 @@ def test_get_accessioning_properties_with_none(self):
 parameters.taxonomyAccession=9906
 parameters.vcfAggregation=BASIC
 parameters.vcf=/path/to/vcf_file.vcf
-parameters.outputVcf=
+parameters.outputVcf=/path/to/output_vcf.vcf
+parameters.duplicateSSAccFile=/path/to/duplicate_ss_acc_file.vcf
 
 accessioning.submitted.categoryId=ss
 accessioning.clustered.categoryId=rs
@@ -397,9 +400,9 @@ def test_get_accessioning_properties_with_none(self):
 recovery.cutoff.days=9999999
 '''
         assert self.prop.get_accessioning_properties(
-            target_assembly='GCA_00000001.1', fasta=None,
-            assembly_report=None, project_accession='PRJEB0001', aggregation='BASIC',
-            taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf') == expected
+            target_assembly='GCA_00000001.1', fasta=None, assembly_report=None, project_accession='PRJEB0001',
+            aggregation='BASIC', taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf',
+            output_vcf='/path/to/output_vcf.vcf', duplicate_ss_acc_file='/path/to/duplicate_ss_acc_file.vcf') == expected
 
     def test_get_release_properties(self):
         expected = '''spring.data.mongodb.uri=mongodb://mongouser:mongop%40ssword@mongos-host1.example.com:27017,mongos-host2.example.com:27017/?retryWrites=true&authSource=admin