easylink 0.1.13__py3-none-any.whl → 0.1.15__py3-none-any.whl

easylink/runner.py

@@ -19,6 +19,7 @@ from snakemake.cli import main as snake_main
 
 from easylink.configuration import Config, load_params_from_specification
 from easylink.pipeline import Pipeline
+from easylink.pipeline_schema import PIPELINE_SCHEMAS, PipelineSchema
 from easylink.utilities.data_utils import (
     copy_configuration_files_to_results_directory,
     create_results_directory,
@@ -30,11 +31,12 @@ from easylink.utilities.paths import EASYLINK_TEMP
 
 def main(
     command: str,
-    pipeline_specification: str,
-    input_data: str,
-    computing_environment: str | None,
-    results_dir: str,
+    pipeline_specification: str | Path,
+    input_data: str | Path,
+    computing_environment: str | Path | None,
+    results_dir: str | Path,
     debug=False,
+    potential_schemas: PipelineSchema | list[PipelineSchema] = PIPELINE_SCHEMAS,
 ) -> None:
     """Runs an EasyLink command.
 
@@ -44,8 +46,8 @@ def main(
     files and then calls on `Snakemake <https://snakemake.readthedocs.io/en/stable/>`_
     to act as the workflow manager.
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     command
         The command to run. Current supported commands include "run" and "generate_dag".
     pipeline_specification
@@ -61,11 +63,14 @@ def main(
     debug
         If False (the default), will suppress some of the workflow output. This
         is intended to only be used for testing and development purposes.
+    potential_schemas
+        A list of potential schemas to validate the pipeline configuration against.
+        This is primarily used for testing purposes. Defaults to the supported schemas.
     """
     config_params = load_params_from_specification(
         pipeline_specification, input_data, computing_environment, results_dir
     )
-    config = Config(config_params)
+    config = Config(config_params, potential_schemas)
     pipeline = Pipeline(config)
     # After validation is completed, create the results directory
     create_results_directory(Path(results_dir))
@@ -84,7 +89,7 @@ def main(
     environment_args = _get_environment_args(config)
     singularity_args = _get_singularity_args(config)
     # Set source cache in appropriate location to avoid jenkins failures
-    os.environ["XDG_CACHE_HOME"] = results_dir + "/.snakemake/source_cache"
+    os.environ["XDG_CACHE_HOME"] = str(results_dir) + "/.snakemake/source_cache"
     # We need to set a dummy environment variable to avoid logging a wall of text.
     # TODO [MIC-4920]: Remove when https://github.com/snakemake/snakemake-interface-executor-plugins/issues/55 merges
     os.environ["foo"] = "bar"
@@ -92,7 +97,7 @@ def main(
         "--snakefile",
         str(snakefile),
         "--directory",
-        results_dir,
+        str(results_dir),
         "--cores",
         "all",
         "--jobs",