change naming of generated pipeline_interface.yaml #417

pepkit · Oct 10, 2023 · f651045 · f651045
1 parent 975c2ca
commit f651045
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/looper/cli_looper.py b/looper/cli_looper.py
@@ -24,6 +24,7 @@
     read_looper_config_file,
     read_yaml_file,
     initiate_looper_config,
+    init_generic_pipeline,
 )
 
 

diff --git a/looper/const.py b/looper/const.py
@@ -205,7 +205,7 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
 EXAMPLE_COMPUTE_SPEC_FMT = "k1=v1 k2=v2"
 SUBMISSION_FAILURE_MESSAGE = "Cluster resource failure"
 LOOPER_DOTFILE_NAME = "." + LOOPER_KEY + ".yaml"
-LOOPER_GENERIC_PIPELINE = "generic_pipeline_interface.yaml"
+LOOPER_GENERIC_PIPELINE = "pipeline_interface.yaml"
 POSITIONAL = [PEP_CONFIG_FILE_KEY, "command"]
 SELECTED_COMPUTE_PKG = "package"
 EXTRA_KEY = "_cli_extra"

diff --git a/looper/utils.py b/looper/utils.py
@@ -337,10 +337,10 @@ def init_generic_pipeline():
 
     # Determine Generic Pipeline Interface
     generic_pipeline_dict = {
-        "pipeline_name": "count_lines",
+        "pipeline_name": "default_pipeline_name",
         "pipeline_type": "sample",
         "output_schema": "output_schema.yaml",
-        "var_templates": {"pipeline": "{looper.piface_dir}/count_lines.sh"},
+        "var_templates": {"pipeline": "{looper.piface_dir}/pipeline.sh"},
         "command_template": "{pipeline.var_templates.pipeline} {sample.file} "
         "--output-parent {looper.sample_output_folder}",
     }
@@ -349,10 +349,10 @@ def init_generic_pipeline():
     if not os.path.exists(dest_file):
         with open(dest_file, "w") as file:
             yaml.dump(generic_pipeline_dict, file)
-        print(f"Generic pipeline interface successfully created at: {dest_file}")
+        print(f"Pipeline interface successfully created at: {dest_file}")
     else:
         print(
-            f"Generic pipeline interface file already exists `{dest_file}`. Skipping creation.."
+            f"Pipeline interface file already exists `{dest_file}`. Skipping creation.."
         )
 
     return True