Snakemake：尝试实现 Jupyter 笔记本时'Unexpected keyword notebook in rule definition'

Question

我一直在尝试使用SnakemakeJupyter笔记本的Snakemake功能，使用SnakeMAKEWiki中给出的示例作为模板(请参阅：Jupyter记事本集成(。

然而，当我尝试运行我的Snakefile时，我得到了错误：Unexpected keyword notebook in rule definition (Snakefile, line 62)。根据我使用Snakemake的经验，这种错误通常是由不一致的缩进引起的，但我一直无法用这种方式解决这个问题。

非常感谢任何帮助

完整Snakefile:

# CONFIG
configfile: "config.yaml"
# PIPELINE RULES.
#include: "rules/preperation/get_remote_genome.snakefile"
include: "rules/preperation/get_remote_annovar_dbs.snakefile"
include: "rules/preperation/bwa_index.snakefile"
include: "rules/fastqc.snakefile"
include: "rules/trimmomatic.snakefile"
include: "rules/bwa_mem.snakefile"
include: "rules/samtools_sort.snakefile"
include: "rules/marked_duplicates.snakefile"
include: "rules/bamtools_split.snakefile"
include: "rules/samtools_mpileup.snakefile"
include: "rules/varscan.snakefile"
include: "rules/concat_vcf.snakefile"
include: "rules/annovar.snakefile"
rule all:
input:
expand("runs/{sample}/results/results_notebook.html",
sample=config["samples"])
rule jupyter_to_html:
input:
"runs/{sample}/results/results_notebook.ipynb"
output:
"runs/{sample}/results/results_notebook.html"
shell:
"jupyter nbconvert --execute --to html {input}"
rule jupyter_report:
input:
expand("runs/{{sample}}/results/{{sample}}_{num}_fastqc.html",
num = ["R1", "R2"]),
expand("runs/{{sample}}/results/{{sample}}.{genome_build}_multianno.txt",
genome_build = config["genome_build"])
output:
"runs/{sample}/results/results_notebook.ipynb"
log:
notebook = "runs/{sample}/results/results_notebook.ipynb"
notebook:
config["notebook"]

Answer 1

Snakemake 5.10以后提供笔记本集成。也许你的Snakemake版本是<5.10？