Python 3.x snakemake snakefile中的语法错误
我试着运行snakemake来测试一个小任务。代码如下: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=
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}'