snakemake snakefile 中的语法错误

Question

我试图运行 snakemake 来测试一个小作业。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}'

当我运行这个时，我得到语法错误：

SyntaxError in line 4 of /fullpath/snakemake-example/Snakefile:
invalid syntax

参考snakemake手册，我看不出任何语法错误。这里会有什么问题？

提前致谢。

Answer 1

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

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}'

snakemake snakefile 中的语法错误

Syntax error in snakemake snakefile

python-3.x

snakemake