fix: properly use configfiles specified via CLI also if configfile specified via configfile directive is not present

johanneskoester · johanneskoester · commit 1e0649ac3717 · 2022-04-26T15:51:25.000+02:00
diff --git a/snakemake/workflow.py b/snakemake/workflow.py
@@ -1315,6 +1315,9 @@ def configfile(self, fp):
                         fp
                     )
                 )
+            else:
+                # CLI configfiles have been specified, do not throw an error but update with their values
+                update_config(self.config, self.overwrite_config)
 
     def set_pepfile(self, path):
 

Original file line number	Diff line number	Diff line change
`@@ -1315,6 +1315,9 @@ def configfile(self, fp):`
`1315`	`1315`	`fp`
`1316`	`1316`	`)`
`1317`	`1317`	`)`
	`1318`	`+ else:`
	`1319`	`+ # CLI configfiles have been specified, do not throw an error but update with their values`
	`1320`	`+ update_config(self.config, self.overwrite_config)`
`1318`	`1321`
`1319`	`1322`	`def set_pepfile(self, path):`
`1320`	`1323`