Commit 227f3d25 authored by bow's avatar bow
Browse files

Update itd-flt3 output bams and RG header value

parent c6d46661
......@@ -7,9 +7,8 @@ include: "includes/itd-flt3/Snakefile"
rule all:
input:
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")],
fqs=expand(RUN.output("{sample}/{sample}-{pair}.fq.gz"), sample=RUN.samples, pair={"R1", "R2"}),
flt3_bam=expand(RUN.output("{sample}/itd-flt3/{sample}.flt3.bam"), 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),
......@@ -22,21 +22,21 @@ rule align_flt3:
fq2=RUN.output("{sample}/{sample}-R2.fq.gz"),
index=RUN.settings["flt3_ref"]
output:
bam=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bam"),
bai=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bai"),
bam=RUN.output("{sample}/itd-flt3/{sample}.flt3.bam"),
bai=RUN.output("{sample}/itd-flt3/{sample}.flt3.bai"),
params:
rg="@RG\tID:{sample}\tSM:{sample}"
rg="@RG\\tID:{sample}\\tSM:{sample}"
threads: 3
conda: srcdir("envs/align_flt3.yml")
shell:
"bwa mem -t {threads} -L 2,2 {input.index} {input.fq1} {input.fq2}"
"bwa mem -R \'{params.rg}\' -t {threads} -L 2,2 {input.index} {input.fq1} {input.fq2}"
" | samtools view -Sbh -F 0x4 -"
" | picard SortSam I=/dev/stdin O={output.bam} SO=coordinate CREATE_INDEX=true"
rule extract_sc_flt3:
input:
bam=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bam"),
bai=RUN.output("{sample}/itd-flt3/{sample}.flt3.sorted.bai"),
bam=RUN.output("{sample}/itd-flt3/{sample}.flt3.bam"),
bai=RUN.output("{sample}/itd-flt3/{sample}.flt3.bai"),
ref=RUN.settings["flt3_ref"],
scr=RUN.settings["extract_sc_flt3"],
output:
......
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