Rename itd tools based on upstream changes

config-base.yml

@@ -64,10 +64,10 @@ settings:
   # kmt2a_start: 456
   # kmt2a_end: 4719
 
-  # Path to the `fidus` executable used for detection of FLT3 ITD.
-  #fidus_exe:
+  # Path to the `rose-dt` executable used for detection of FLT3 ITD.
+  #rose_dt_exe:
 
-  # Path to the `fidus-plot.py` script used for plotting FLT3 ITD detection results.
+  # Path to the `rose-dt-plot.py` script used for plotting FLT3 ITD detection results.
   #plot_itd:
 
   # Path to the conda environment file specifying the `fidus-plot.py` script dependencies.

includes/itd/Snakefile.flt3

@@ -4,8 +4,6 @@ from rattle import Run
 
 RUN = Run(config)
 
-# TODO: deploy fidus_exe and plot script properly
-
 # Region of interest ~ exon 14-15 in transcript coordinates.
 RUN.set_default_setting("flt3_name", "FLT3-001")
 RUN.set_default_setting("flt3_start", 1787)
@@ -39,7 +37,7 @@ rule detect_flt3:
         bam=RUN.output("{sample}/itd/{sample}.flt3.bam"),
         bai=RUN.output("{sample}/itd/{sample}.flt3.bai"),
         ref=RUN.settings["flt3_fasta"],
-        exe=RUN.settings["fidus_exe"],
+        exe=RUN.settings["rose_dt_exe"],
     output:
         csv=RUN.output("{sample}/itd/{sample}.flt3.csv"),
         bg_csv=RUN.output("{sample}/itd/{sample}.flt3.bg.csv"),

includes/itd/Snakefile.kmt2a

@@ -37,7 +37,7 @@ rule detect_kmt2a:
         bam=RUN.output("{sample}/itd/{sample}.kmt2a.bam"),
         bai=RUN.output("{sample}/itd/{sample}.kmt2a.bai"),
         ref=RUN.settings["kmt2a_fasta"],
-        exe=RUN.settings["fidus_exe"],
+        exe=RUN.settings["rose_dt_exe"],
     output:
         csv=RUN.output("{sample}/itd/{sample}.kmt2a.csv"),
         bg_csv=RUN.output("{sample}/itd/{sample}.kmt2a.bg.csv"),