Collect target coverage disabled when no target coverage files requested

bihealth · Jun 29, 2022 · 15cd954 · 15cd954
1 parent be05d60
commit 15cd954
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py
@@ -1269,9 +1269,11 @@ def get_result_files(self):
             )
         )
 
+        target_coverage = False
         for sheet in self.shortcut_sheets:
             for ngs_library in sheet.all_ngs_libraries:
                 if ngs_library.name in self.ngs_library_to_kit:
+                    target_coverage = True
                     extraction_type = ngs_library.test_sample.extra_infos["extractionType"]
                     suffix = (
                         "_long"
@@ -1287,8 +1289,9 @@ def get_result_files(self):
                         ngs_library=[ngs_library],
                         ext=["txt", "txt.md5"],
                     )
-        yield "output/target_cov_report/out/target_cov_report.txt"
-        yield "output/target_cov_report/out/target_cov_report.txt.md5"
+        if target_coverage:
+            yield "output/target_cov_report/out/target_cov_report.txt"
+            yield "output/target_cov_report/out/target_cov_report.txt.md5"
         if (
             self.config["picard_hs_metrics"]["path_targets_interval_list"]
             and self.config["picard_hs_metrics"]["path_baits_interval_list"]