fix: 355 wgs svcnv export external are also affected by changes in th…

…e wrapper for varfish annotator (#356)
bihealth · Jan 18, 2023 · a660bda · a660bda
1 parent e50d4d4
commit a660bda
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Showing 5 changed files with 416 additions and 17 deletions.
diff --git a/snappy_pipeline/workflows/wgs_cnv_export_external/__init__.py b/snappy_pipeline/workflows/wgs_cnv_export_external/__init__.py
@@ -195,6 +195,7 @@ def _get_output_files_annotate(self):
             key = infix.replace("-", "_")
             yield key, prefix + f".{infix}.tsv.gz"
             yield key + "_md5", prefix + f".{infix}.tsv.gz.md5"
+        yield "output_links", []
 
     def get_log_file(self, action):
         self._validate_action(action)
@@ -224,17 +225,15 @@ def _get_log_file_annotate(self):
             "varfish_annotated.{index_ngs_library}"
         )
         key_ext = (
-            ("wrapper", ".wrapper.py"),
-            ("wrapper_md5", ".wrapper.py.md5"),
             ("log", ".log"),
-            ("log_md5", ".log.md5"),
             ("conda_info", ".conda_info.txt"),
-            ("conda_info_md5", ".conda_info.txt.md5"),
             ("conda_list", ".conda_list.txt"),
-            ("conda_list_md5", ".conda_list.txt.md5"),
+            ("wrapper", ".wrapper.py"),
+            ("env_yaml", ".environment.yaml"),
         )
         for key, ext in key_ext:
             yield key, prefix + ext
+            yield key + "_md5", prefix + ext + ".md5"
 
     def get_resource_usage(self, action):
         """Get Resource Usage
@@ -388,6 +387,10 @@ def get_result_files(self):
                 ".conda_info.txt.md5",
                 ".conda_list.txt",
                 ".conda_list.txt.md5",
+                ".wrapper.py",
+                ".wrapper.py.md5",
+                ".environment.yaml",
+                ".environment.yaml.md5",
             ),
         )
 

diff --git a/snappy_pipeline/workflows/wgs_sv_export_external/__init__.py b/snappy_pipeline/workflows/wgs_sv_export_external/__init__.py
@@ -195,6 +195,7 @@ def _get_output_files_annotate(self):
             key = infix.replace("-", "_")
             yield key, prefix + f".{infix}.tsv.gz"
             yield key + "_md5", prefix + f".{infix}.tsv.gz.md5"
+        yield "output_links", []
 
     def get_log_file(self, action):
         self._validate_action(action)
@@ -224,17 +225,15 @@ def _get_log_file_annotate(self):
             "varfish_annotated.{index_ngs_library}"
         )
         key_ext = (
-            ("wrapper", ".wrapper.py"),
-            ("wrapper_md5", ".wrapper.py.md5"),
             ("log", ".log"),
-            ("log_md5", ".log.md5"),
             ("conda_info", ".conda_info.txt"),
-            ("conda_info_md5", ".conda_info.txt.md5"),
             ("conda_list", ".conda_list.txt"),
-            ("conda_list_md5", ".conda_list.txt.md5"),
+            ("wrapper", ".wrapper.py"),
+            ("env_yaml", ".environment.yaml"),
         )
         for key, ext in key_ext:
             yield key, prefix + ext
+            yield key + "_md5", prefix + ext + ".md5"
 
     def get_resource_usage(self, action):
         """Get Resource Usage
@@ -387,6 +386,10 @@ def get_result_files(self):
                 ".conda_info.txt.md5",
                 ".conda_list.txt",
                 ".conda_list.txt.md5",
+                ".wrapper.py",
+                ".wrapper.py.md5",
+                ".environment.yaml",
+                ".environment.yaml.md5",
             ),
         )
 

diff --git a/snappy_wrappers/wrappers/varfish_annotator/annotate_svs/wrapper.py b/snappy_wrappers/wrappers/varfish_annotator/annotate_svs/wrapper.py
@@ -5,7 +5,8 @@
 __author__ = "Manuel Holtgrewe <[email protected]>"
 
 # Get shortcut to configuration of varfish_export step
-export_config = snakemake.config["step_config"]["varfish_export"]
+step_name = snakemake.params.args["step_name"]
+export_config = snakemake.config["step_config"][step_name]
 # Get shortcut to "fix_manta_invs.py" postprocessing script
 fix_manta_invs = os.path.join(
     os.path.dirname(__file__),