Remove pangolin-nf (#17)

BCCDC-PHL · Jun 29, 2023 · f48db3f · f48db3f
1 parent b26e1d6
commit f48db3f
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Showing 2 changed files with 0 additions and 28 deletions.
diff --git a/auto_ncov/core.py b/auto_ncov/core.py
@@ -254,14 +254,6 @@ def analyze_run(config: dict[str, object], run: dict[str, object]) -> None:
                 elif parameter['flag'] == '--metadata':
                     parameter['value'] = analysis_run_metadata_path
 
-        elif pipeline['pipeline_name'] == 'BCCDC-PHL/pangolin-nf':
-            for dependency in pipeline['dependencies']:
-                if dependency['pipeline_name'] == 'BCCDC-PHL/ncov2019-artic-nf':
-                    artic_version = dependency['pipeline_version']
-                    artic_minor_version = '.'.join(artic_version.lstrip('v').split('.')[0:2])
-            ncov2019_artic_nf_output_dir = "ncov2019-artic-nf-v" + artic_minor_version + "-output"
-            analysis_pipeline_output_dir = os.path.abspath(os.path.join(analysis_run_output_dir, ncov2019_artic_nf_output_dir, analysis_output_dir_name))
-
         else:
             # We only want to run the three pipelines listed above. Skip anything else.
             continue

diff --git a/config_template.json b/config_template.json
@@ -122,26 +122,6 @@
                     "value": null
                 }
             ]
-        },
-        {
-            "pipeline_name": "BCCDC-PHL/pangolin-nf",
-            "pipeline_version": "v0.2.0",
-            "dependencies": [
-                {
-                    "pipeline_name": "BCCDC-PHL/ncov2019-artic-nf",
-                    "pipeline_version": "v1.3.3"
-                }
-            ],
-            "pipeline_parameters": [
-                {
-                    "flag": "--analysis_parent_dir",
-                    "value": "/path/to/analysis_by_run"
-                },
-                {
-                    "flag": "--outdir",
-                    "value": null
-                }
-            ]
         }
     ]
 }