diff --git a/scripts/aviti_run_parameter_parser.py b/scripts/aviti_run_parameter_parser.py index 78bc45e8..20268681 100644 --- a/scripts/aviti_run_parameter_parser.py +++ b/scripts/aviti_run_parameter_parser.py @@ -161,12 +161,14 @@ def set_run_stats(process, run_dir): for art in process.all_outputs(): if "Lane" in art.name: lane_nbr = int(art.name.split(" ")[1]) - lane_stats = run_stats["LaneStats"][lane_nbr-1] + lane_stats = run_stats["LaneStats"][lane_nbr - 1] for read in lane_stats["Reads"]: read_key = read["Read"] art.udf[f"Reads PF (M) {read_key}"] = lane_stats["PFCount"] / 1000000 art.udf[f"%PF {read_key}"] = lane_stats["PercentPF"] - art.udf[f"Yield PF (Gb) {read_key}"] = lane_stats["TotalYield"] / 1000000000 + art.udf[f"Yield PF (Gb) {read_key}"] = ( + lane_stats["TotalYield"] / 1000000000 + ) art.udf[f"% Aligned {read_key}"] = read["PhiXAlignmentRate"] art.udf[f"% Bases >=Q30 {read_key}"] = calculate_mean( read["Cycles"], "PercentQ30"