Merge pull request #490 from genomic-medicine-sweden/version_fix

fix: bugfix of version crash when pipeline runs over several days
genomic-medicine-sweden · Sep 25, 2024 · 22343da · 22343da
2 parents a7589c7 + 48255ed
commit 22343da
Showing 1 changed file with 12 additions and 8 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -31,7 +31,7 @@ from hydra_genetics.utils.software_versions import touch_software_version_file
 from hydra_genetics.utils.software_versions import use_container
 
 
-hydra_min_version("1.14.0")
+hydra_min_version("3.0.0")
 
 min_version("7.13.0")
 
@@ -74,20 +74,24 @@ with open(config["output"]) as output:
 
 validate(output_spec, schema="../schemas/output_files.schema.yaml")
 
-date_string = datetime.now().strftime("%Y%m%d")
-pipeline_version = get_pipeline_version(workflow, pipeline_name="Twist_Solid")
-version_files = touch_pipeline_version_file_name(pipeline_version, date_string=date_string, directory="results/versions/software")
+## get version information on pipeline, containers and software
+
+pipeline_name = "Twist_Solid"
+pipeline_version = get_pipeline_version(workflow, pipeline_name=pipeline_name)
+version_files = touch_pipeline_version_file_name(
+    pipeline_version, date_string=pipeline_name, directory="results/versions/software"
+)
 if use_container(workflow):
-    version_files.append(touch_software_version_file(config, date_string=date_string, directory="results/versions/software"))
+    version_files.append(touch_software_version_file(config, date_string=pipeline_name, directory="results/versions/software"))
 add_version_files_to_multiqc(config, version_files)
 
 
 onstart:
-    export_pipeline_version_as_file(pipeline_version, date_string=date_string, directory="results/versions/software")
+    export_pipeline_version_as_file(pipeline_version, date_string=pipeline_name, directory="results/versions/software")
     if use_container(workflow):
         update_config, software_info = add_software_version_to_config(config, workflow, False)
-        export_software_version_as_file(software_info, date_string=date_string, directory="results/versions/software")
-    export_config_as_file(update_config, date_string=date_string, directory="results/versions")
+        export_software_version_as_file(software_info, date_string=pipeline_name, directory="results/versions/software")
+    export_config_as_file(update_config, date_string=pipeline_name, directory="results/versions")
 
 
 ### Set wildcard constraints