Commit e36da3da authored by bow's avatar bow
Browse files

Update output dir of itd-flt3 include

parent 08ba69c9
......@@ -10,6 +10,6 @@ rule all:
fqs=[RUN.output("{sample}/{sample}-{pair}.fq.gz", fmt=True,
sample=unit.sample, pair=pair)
for unit in RUN.unit_names for pair in ("R1", "R2")],
flt3_sc_jsons=expand(RUN.output("{sample}/{sample}.flt3-sc.json"), sample=RUN.samples),
flt3_sc_plots=expand(RUN.output("{sample}/{sample}.flt3-sc.png"), sample=RUN.samples),
flt3_sc_jsons=expand(RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.json"), sample=RUN.samples),
flt3_sc_plots=expand(RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.png"), sample=RUN.samples),
......@@ -13,8 +13,8 @@ RUN.set_default_setting("plot_sc_linear_flt3",
rule all_flt3:
input:
flt3_sc_jsons=expand(RUN.output("{sample}/{sample}.flt3-sc.json"), sample=RUN.samples),
flt3_sc_plots=expand(RUN.output("{sample}/{sample}.flt3-sc.png"), sample=RUN.samples),
flt3_sc_jsons=expand(RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.json"), sample=RUN.samples),
flt3_sc_plots=expand(RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.png"), sample=RUN.samples),
rule align_flt3:
input:
......@@ -22,8 +22,8 @@ rule align_flt3:
fq2=RUN.output("{sample}/{sample}-R2.fq.gz"),
index=RUN.settings["flt3_ref"]
output:
bam=RUN.output("{sample}/{sample}.flt3.sorted.bam"),
bai=RUN.output("{sample}/{sample}.flt3.sorted.bai"),
bam=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bam"),
bai=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bai"),
params:
rg="@RG\tID:{sample}\tSM:{sample}"
threads: 3
......@@ -35,12 +35,12 @@ rule align_flt3:
rule extract_sc_flt3:
input:
bam=RUN.output("{sample}/{sample}.flt3.sorted.bam"),
bai=RUN.output("{sample}/{sample}.flt3.sorted.bai"),
bam=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bam"),
bai=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bai"),
ref=RUN.settings["flt3_ref"],
scr=RUN.settings["extract_sc_flt3"],
output:
json=RUN.output("{sample}/{sample}.flt3-sc.json"),
json=RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.json"),
conda: srcdir("envs/extract_sc_flt3.yml")
threads: 2
shell:
......@@ -49,10 +49,10 @@ rule extract_sc_flt3:
rule plot_sc_linear_flt3:
input:
counts=RUN.output("{sample}/{sample}.flt3-sc.json"),
counts=RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.json"),
scr=RUN.settings["plot_sc_linear_flt3"],
output:
png=RUN.output("{sample}/{sample}.flt3-sc.png"),
png=RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.png"),
conda: srcdir("envs/plot_sc_linear_flt3.yml")
shell:
"python {input.scr} --min-sc-count 2 --min-insert-count 2 --fuzziness 12 --padding 50"
......
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