From d137ffc648bfc51ed370dcb40df1864c151910c7 Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Mon, 19 Aug 2024 11:22:42 -0400 Subject: [PATCH] fix: removed ifelse from targets; simplfied custom target code --- src/xavier/gui.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/xavier/gui.py b/src/xavier/gui.py index bd24a6c..37390bf 100644 --- a/src/xavier/gui.py +++ b/src/xavier/gui.py @@ -258,7 +258,7 @@ def launch_gui(DEBUG=True): window.Element("-OUTDIR-").update("") continue if values["-CUSTARG-"] == True: - if values["-TARGETS-"] == "": + if not values["-TARGETS-"]: sg.PopupError( "Custom Targets BED file selected but not provided!!", location=(0, 500), @@ -281,9 +281,7 @@ def launch_gui(DEBUG=True): input=list(glob.glob(os.path.join(values["-INDIR-"], "*.fastq.gz"))), output=output_dir, genome=genome, - targets=values["-TARGETS-"] - if values["-TARGETS-"] - else (""), # TODO should this be part of the genome config file? + targets=values["-TARGETS-"], mode="slurm", job_name="pl:xavier", callers=["mutect2", "mutect", "strelka", "vardict", "varscan"],