Commit ea202861 authored by bow's avatar bow
Browse files

Rename itd tools based on upstream changes

parent 9849bd3e
...@@ -64,10 +64,10 @@ settings: ...@@ -64,10 +64,10 @@ settings:
# kmt2a_start: 456 # kmt2a_start: 456
# kmt2a_end: 4719 # kmt2a_end: 4719
# Path to the `fidus` executable used for detection of FLT3 ITD. # Path to the `rose-dt` executable used for detection of FLT3 ITD.
#fidus_exe: #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: #plot_itd:
# Path to the conda environment file specifying the `fidus-plot.py` script dependencies. # Path to the conda environment file specifying the `fidus-plot.py` script dependencies.
......
...@@ -4,8 +4,6 @@ from rattle import Run ...@@ -4,8 +4,6 @@ from rattle import Run
RUN = Run(config) RUN = Run(config)
# TODO: deploy fidus_exe and plot script properly
# Region of interest ~ exon 14-15 in transcript coordinates. # Region of interest ~ exon 14-15 in transcript coordinates.
RUN.set_default_setting("flt3_name", "FLT3-001") RUN.set_default_setting("flt3_name", "FLT3-001")
RUN.set_default_setting("flt3_start", 1787) RUN.set_default_setting("flt3_start", 1787)
...@@ -39,7 +37,7 @@ rule detect_flt3: ...@@ -39,7 +37,7 @@ rule detect_flt3:
bam=RUN.output("{sample}/itd/{sample}.flt3.bam"), bam=RUN.output("{sample}/itd/{sample}.flt3.bam"),
bai=RUN.output("{sample}/itd/{sample}.flt3.bai"), bai=RUN.output("{sample}/itd/{sample}.flt3.bai"),
ref=RUN.settings["flt3_fasta"], ref=RUN.settings["flt3_fasta"],
exe=RUN.settings["fidus_exe"], exe=RUN.settings["rose_dt_exe"],
output: output:
csv=RUN.output("{sample}/itd/{sample}.flt3.csv"), csv=RUN.output("{sample}/itd/{sample}.flt3.csv"),
bg_csv=RUN.output("{sample}/itd/{sample}.flt3.bg.csv"), bg_csv=RUN.output("{sample}/itd/{sample}.flt3.bg.csv"),
......
...@@ -37,7 +37,7 @@ rule detect_kmt2a: ...@@ -37,7 +37,7 @@ rule detect_kmt2a:
bam=RUN.output("{sample}/itd/{sample}.kmt2a.bam"), bam=RUN.output("{sample}/itd/{sample}.kmt2a.bam"),
bai=RUN.output("{sample}/itd/{sample}.kmt2a.bai"), bai=RUN.output("{sample}/itd/{sample}.kmt2a.bai"),
ref=RUN.settings["kmt2a_fasta"], ref=RUN.settings["kmt2a_fasta"],
exe=RUN.settings["fidus_exe"], exe=RUN.settings["rose_dt_exe"],
output: output:
csv=RUN.output("{sample}/itd/{sample}.kmt2a.csv"), csv=RUN.output("{sample}/itd/{sample}.kmt2a.csv"),
bg_csv=RUN.output("{sample}/itd/{sample}.kmt2a.bg.csv"), bg_csv=RUN.output("{sample}/itd/{sample}.kmt2a.bg.csv"),
......
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