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Python 3.x snakemake snakefile中的语法错误_Python 3.x_Snakemake - Fatal编程技术网

Python 3.x snakemake snakefile中的语法错误

Python 3.x snakemake snakefile中的语法错误,python-3.x,snakemake,Python 3.x,Snakemake,我试着运行snakemake来测试一个小任务。代码如下: rule kallisto_quant: input: idx='/fullpath/snakemake-example/Kallisto_test/Arabidopsis_thaliana.fa.index' fwd='/fullpath/snakemake-example/Kallisto_test/Condition1_R1_008.trimmed.fastq.gz' rvs=

我试着运行snakemake来测试一个小任务。代码如下:

rule kallisto_quant:
    input:
        idx='/fullpath/snakemake-example/Kallisto_test/Arabidopsis_thaliana.fa.index'
        fwd='/fullpath/snakemake-example/Kallisto_test/Condition1_R1_008.trimmed.fastq.gz'
        rvs='/fullpath/snakemake-example/Kallisto_test/Condition1_R2_008.trimmed.fastq.gz'
    output:
        '/Condition1'
    threads: 10
    shell:
        'kallisto quant -i {input.idx} -o {output} -b 100 {input.fwd} {input.rvs}'
当我运行此命令时,会出现语法错误:

SyntaxError in line 4 of /fullpath/snakemake-example/Snakefile:
invalid syntax
通过参考snakemake手册,我看不到任何语法错误。这里有什么问题


提前感谢。

输入中缺少逗号。另外,我相信snakemake要求
输出
是文件而不是目录,这就是您在示例中使用的

rule kallisto_quant:
    input:
        idx='/fullpath/snakemake-example/Kallisto_test/Arabidopsis_thaliana.fa.index',
        fwd='/fullpath/snakemake-example/Kallisto_test/Condition1_R1_008.trimmed.fastq.gz',
        rvs='/fullpath/snakemake-example/Kallisto_test/Condition1_R2_008.trimmed.fastq.gz'
    output:
        '/Condition1'
    threads: 10
    shell:
        'kallisto quant -i {input.idx} -o {output} -b 100 {input.fwd} {input.rvs}'