在 snakemake 中的多个输入之前添加标志 -I

Question

我正在使用 snakemake 来描述 GATK 管道。我需要运行以下命令：

./../gatk-4.1.3.0/gatk --java-options ""-Xmx7680m""  GatherBQSRReports  -I file1 -I file2 -I file3 -O output

相反，我得到了以下结果：

./../gatk-4.1.3.0/gatk --java-options ""-Xmx7680m""  GatherBQSRReports  -I file1 file2 file3 -O output

现在我的代码如下所示：

import glob
SAMPLES = glob_wildcards("input_bam/{sample}.bam")
INTERVALS = glob_wildcards("../intervals/{interval}.bed")

rule all:
        input: expand("out/{sample}.AddOrReplaceReadGroups.bam", sample = SAMPLES.sample), expand("out/{sample}.MarkDuplicates.bam", sample=SAMPLES.sample),,expand("out_BaseRecalibrator/{sample}.BaseRecalibrator.{interval}.txt", interval=INTERVALS.interval, sample=SAMPLES.sample), expand("out_BaseRecalibrator/{sample}.GatherBQSRReports.txt", sample=SAMPLES.sample)

rule gatk_AddOrReplaceReadGroups:
        input: "input_bam/{sample}.bam"
        output: "out/{sample}.AddOrReplaceReadGroups.bam"
        shell: "./../gatk-4.1.3.0/gatk --java-options ""-Xmx30g"" AddOrReplaceReadGroups -I {input}  -O {output} -ID group1 -SM TUMOR -PL illumina -LB lib1 -PU unit1"

rule gatk_MarkDuplicates:
        input: rules.gatk_AddOrReplaceReadGroups.output
        output: output1="out/{sample}.MarkDuplicates.bam", output2="out/{sample}.MarkDuplicates.txt"
        shell: "./../gatk-4.1.3.0/gatk --java-options ""-Xmx4g""  MarkDuplicates -I {input} -O {output.output1} -M {output.output2} --CREATE_INDEX true"

rule gatk_BaseRecalibrator:
    input: input1="../intervals/{interval}.bed", input2="out/{sample}.MarkDuplicates.bam", input3='../ref/ref.fa', input4="../dbsnp/dbsnp_150.hg38.vcf.gz"
    output: "out_BaseRecalibrator/{sample}.BaseRecalibrator.{interval}.txt"
    shell: "./../gatk-4.1.3.0/gatk --java-options ""-Xmx7680m""  BaseRecalibrator -L {input.input1} -I {input.input2} -O {output} -R {input.input3} --known-sites {input.input4}"

rule gatk_GatherBQSRReports:
        input: expand("out_BaseRecalibrator/{sample}.BaseRecalibrator.{interval}.txt", interval=INTERVALS.interval, sample=SAMPLES.sample)
        output: "out_BaseRecalibrator/{sample}.GatherBQSRReports.txt"
        shell: "./../gatk-4.1.3.0/gatk --java-options ""-Xmx7680m""  GatherBQSRReports  -I {input}  -O {output}"

我是这个程序的新手，不会编写所需的参数。我很乐意提供任何帮助

Answer 1

你可以这样做：

reports = expand("out_BaseRecalibrator/{sample}.BaseRecalibrator.{interval}.txt", interval=INTERVALS.interval, sample=SAMPLES.sample)

rule gatk_GatherBQSRReports:
        input:
            reports,
        params:
            reports= '-I ' + ' -I '.join(reports),
        output:
            ...
        shell: 
            r"""
            ./../gatk-4.1.3.0/gatk --java-options -Xmx7680m  GatherBQSRReports {params.reports}  -O {output}
            """

在 snakemake 中的多个输入之前添加标志 -I

Add flag -I before multiple input in snakemake

snakemake