Check that VEP has been run correctly (#208)

* Check that VEP has been run correctly * fix tests
EBIvariation · Jul 2, 2024 · 5aafb7c · 5aafb7c
1 parent 604d9d7
commit 5aafb7c
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Showing 4 changed files with 10 additions and 1 deletion.
diff --git a/eva_submission/submission_qc_checks.py b/eva_submission/submission_qc_checks.py
@@ -287,7 +287,7 @@ def check_if_variant_load_completed_successfully(self, vcf_files):
             ]
             # annotation only happens if a VEP cache can be found
             assembly_accession = self.eload_cfg.query('brokering', 'analyses', analysis_alias, 'assembly_accession')
-            if self.eload_cfg.query('ingestion', 'vep', assembly_accession, 'cache_version') == None:
+            if self.eload_cfg.query('ingestion', 'vep', assembly_accession, 'cache_version') is not None:
                 self._find_log_and_check_job(
                     analysis_accession, f"annotation.*{analysis_accession}*.log", "annotate_variants", failed_analysis
                 )

diff --git a/tests/resources/eloads/ELOAD_101/.ELOAD_101_config.yml b/tests/resources/eloads/ELOAD_101/.ELOAD_101_config.yml
@@ -20,6 +20,9 @@ brokering:
     hold_date: 2021-01-04
 ingestion:
   project_dir: tests/resources/projects/PRJEB11111
+  vep:
+    GCA_000001000.1:
+      cache_version: 1
 submission:
   analyses:
     Analysis alias test:

diff --git a/tests/resources/eloads/ELOAD_102/.ELOAD_102_config.yml b/tests/resources/eloads/ELOAD_102/.ELOAD_102_config.yml
@@ -20,6 +20,9 @@ brokering:
     hold_date: 2021-01-04
 ingestion:
   project_dir: tests/resources/projects/PRJEB22222
+  vep:
+    GCA_000001000.1:
+      cache_version: 1
 submission:
   analyses:
     Analysis alias test:

diff --git a/tests/resources/eloads/ELOAD_104/.ELOAD_104_config.yml b/tests/resources/eloads/ELOAD_104/.ELOAD_104_config.yml
@@ -18,6 +18,9 @@ ingestion:
   project_dir: tests/resources/projects/PRJEB44444
   remap_and_cluster:
     target_assembly: GCA_000247795.2
+  vep:
+    GCA_000003205.6:
+      cache_version: 1
 submission:
   analyses:
     Analysis alias test: