VCF validator does not output the database anymore

EBIvariation · Oct 29, 2024 · 042dacc · 042dacc
1 parent 850d0dc
commit 042dacc
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/eva_sub_cli/nextflow/validation.nf b/eva_sub_cli/nextflow/validation.nf
@@ -137,15 +137,14 @@ process check_vcf_valid {
     tuple path(vcf), path(fasta), path(report)
 
     output:
-    path "vcf_format/*.errors.*.db", emit: vcf_validation_db
     path "vcf_format/*.errors.*.txt", emit: vcf_validation_txt
     path "vcf_format/*.vcf_format.log", emit: vcf_validation_log
 
     """
     trap 'if [[ \$? == 1 ]]; then exit 0; fi' EXIT
 
     mkdir -p vcf_format
-    $params.executable.vcf_validator -i $vcf -r database,text -o vcf_format --require-evidence > vcf_format/${vcf}.vcf_format.log 2>&1
+    $params.executable.vcf_validator -i $vcf -r text -o vcf_format --require-evidence > vcf_format/${vcf}.vcf_format.log 2>&1
     """
 }
 

diff --git a/eva_sub_cli/validators/validator.py b/eva_sub_cli/validators/validator.py
@@ -225,9 +225,8 @@ def _collect_vcf_check_results(self,):
 
             vcf_check_log = self._vcf_check_log(vcf_name)
             vcf_check_text_report = self._vcf_check_text_report(vcf_name)
-            vcf_check_db_report = self._vcf_check_db_report(vcf_name)
 
-            if vcf_check_log and vcf_check_text_report and vcf_check_db_report:
+            if vcf_check_log and vcf_check_text_report:
                 valid, warning_count, error_count, critical_count, error_list, critical_list = parse_vcf_check_report(vcf_check_text_report)
             else:
                 valid, warning_count, error_count, critical_count, error_list, critical_list = (False, 0, 0, 1, [], ['Process failed'])

diff --git a/tests/test_docker_validator.py b/tests/test_docker_validator.py
@@ -101,9 +101,9 @@ def assert_validation_results(self, validator, expected_sample_checker, expected
         with open(vcf_format_log_file) as vcf_format_log_file:
             vcf_format_logs = vcf_format_log_file.readlines()
             self.assertEqual('[info] According to the VCF specification, the input file is valid\n',
-                             vcf_format_logs[3])
+                             vcf_format_logs[2])
 
-            text_report = vcf_format_logs[2].split(':')[1].strip()
+            text_report = vcf_format_logs[1].split(':')[1].strip()
             with open(os.path.join(validator.output_dir, text_report)) as text_report:
                 text_report_content = text_report.readlines()
                 self.assertEqual('According to the VCF specification, the input file is valid\n',