Patch demultiplexing (#2933)(patch)

### Fixed

- Dict keys updated as well

cg/apps/demultiplex/demultiplex_api.py

@@ -34,8 +34,10 @@ def __init__(self, config: dict, housekeeper_api: HousekeeperAPI, out_dir: Path
         self.hk_api = housekeeper_api
         self.slurm_account: str = config["demultiplex"]["slurm"]["account"]
         self.mail: str = config["demultiplex"]["slurm"]["mail_user"]
-        self.flow_cells_dir: Path = Path(config["flow_cells_dir"])
-        self.demultiplexed_runs_dir: Path = out_dir or Path(config["demultiplexed_flow_cells_dir"])
+        self.flow_cells_dir: Path = Path(config["illumina_flow_cells_directory"])
+        self.demultiplexed_runs_dir: Path = out_dir or Path(
+            config["illumina_demultiplexed_runs_directory"]
+        )
         self.environment: str = config.get("environment", "stage")
         LOG.info(f"Set environment to {self.environment}")
         self.dry_run: bool = False

tests/conftest.py

@@ -376,8 +376,8 @@ def demultiplex_configs_for_demux(
 ) -> dict:
     """Return demultiplex configs."""
     return {
-        "flow_cells_dir": tmp_illumina_flow_cells_demux_all_directory.as_posix(),
-        "demultiplexed_flow_cells_dir": tmp_empty_demultiplexed_runs_directory.as_posix(),
+        "illumina_flow_cells_directory": tmp_illumina_flow_cells_demux_all_directory.as_posix(),
+        "illumina_demultiplexed_runs_directory": tmp_empty_demultiplexed_runs_directory.as_posix(),
         "demultiplex": {"slurm": {"account": "test", "mail_user": "[email protected]"}},
     }
 
@@ -389,8 +389,8 @@ def demultiplex_configs(
 ) -> dict:
     """Return demultiplex configs."""
     return {
-        "flow_cells_dir": tmp_illumina_flow_cells_directory.as_posix(),
-        "demultiplexed_flow_cells_dir": tmp_illumina_demultiplexed_flow_cells_directory.as_posix(),
+        "illumina_flow_cells_directory": tmp_illumina_flow_cells_directory.as_posix(),
+        "illumina_demultiplexed_runs_directory": tmp_illumina_demultiplexed_flow_cells_directory.as_posix(),
         "demultiplex": {"slurm": {"account": "test", "mail_user": "[email protected]"}},
     }