Merge pull request #66 from tcezard/update_vcf_validator

Use new version of VCF validator

conda/meta.yaml

@@ -22,7 +22,7 @@ requirements:
     - nextflow >=21.10.0
     - python >=3.8
     - nodejs >=10.19.1
-    - vcf-validator >=0.9.7
+    - vcf-validator >=0.10.0
     - ebi-eva-common-pyutils >=0.6.1
     - pyyaml
     - jinja2

docker/Dockerfile

@@ -1,6 +1,6 @@
 FROM python:3.10
 
-ENV vcf_validator_version=0.9.7
+ENV vcf_validator_version=0.10.0
 ENV NXF_VER=22.10.6
 
 WORKDIR /opt

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
     """
 }
 

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'])

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',