From c4ee1525ebfa4e37b38d9b9ff79fd5a4687e2bc1 Mon Sep 17 00:00:00 2001 From: Vincent Janvid <69356202+Vince-janv@users.noreply.github.com> Date: Mon, 12 Feb 2024 15:05:32 +0100 Subject: [PATCH] Patch demultiplexing (#2933)(patch) ### Fixed - Dict keys updated as well --- cg/apps/demultiplex/demultiplex_api.py | 6 ++++-- tests/conftest.py | 8 ++++---- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/cg/apps/demultiplex/demultiplex_api.py b/cg/apps/demultiplex/demultiplex_api.py index 5759f8ccdb..e109d2cf7e 100644 --- a/cg/apps/demultiplex/demultiplex_api.py +++ b/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 diff --git a/tests/conftest.py b/tests/conftest.py index f1d803132a..2f0580ef39 100644 --- a/tests/conftest.py +++ b/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": "testuser@github.se"}}, } @@ -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": "testuser@github.se"}}, }