Move target_rule to beginning of snakemake call

The target was previously at the end of the call, but then if the last user-provided snakemake argument is something that consumes arguments (such as `-q`), the target gets misinterpreted and snakemake errors.
khanlab · Mar 14, 2023 · 772744b · 772744b
1 parent ca5560b
commit 772744b
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/snakebids/app.py b/snakebids/app.py
@@ -233,16 +233,16 @@ def run_snakemake(self):
                 *filter(
                     None,
                     [
+                        *app.config["targets_by_analysis_level"][
+                            app.config["analysis_level"]
+                        ],
                         "--snakefile",
                         str(app.snakefile_path),
                         "--directory",
                         str(cwd),
                         "--configfile",
                         str(new_config_file.resolve()),
                         *app.config["snakemake_args"],
-                        *app.config["targets_by_analysis_level"][
-                            app.config["analysis_level"]
-                        ],
                     ],
                 )
             ]