英文:
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards error
问题
我有一个类似的Snakemake脚本，当我运行它时，Snakemake报告以下错误：
目标规则不能包含通配符。请指定具体文件或没有通配符的规则。
我不确定出了什么问题，你可以帮助我吗？
英文:
I have a snakemake srcipt like
# minimal example
configfile: "../snakemake/config.yaml"
import os
rule generateInclude:
input:
archaic_inc=config['input']['archaic_include'],
modern_inc=config['input']['modern_include']
output:
all_include='include_{reference_genome}.bed'
params:
reference_genome='{reference_genome}'
shell:
"""
if [ {params.reference_genome}=='hg19' ]; then
bedtools intersect -a <(zcat {input.archaic_inc} | sed 's/^chr//') \
-b <(zcat {input.modern_inc} | sed 's/^chr//') > {output.all_include}
else
bedtools intersect -a <(zcat {input.archaic_inc}) \
-b <(zcat {input.modern_inc}) > {output.all_include}
fi
"""
rule all:
input:
'include_hg19.bed'
When I run it, snakemake report
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.
I am not sure whats wrong with it, could your please gave me some help
答案1
得分: 1
默认情况下，snakemake 使用第一个规则作为目标规则。将规则 all 移动到顶部后，您应该能够运行此文件：
rule all:
input:
'include_hg19.bed';
rule generateInclude:
...
英文:
By default snakemake uses the first rule as the target rule. By moving rule all to the top, you should be able to run this file:
rule all:
input:
'include_hg19.bed'
rule generateInclude:
...
通过集体智慧和协作来改善编程学习和解决问题的方式。致力于成为全球开发者共同参与的知识库，让每个人都能够通过互相帮助和分享经验来进步。
评论