python - 如何在snakemake中修复这个“IndexError：list index out of range”

Question

标签： pythonsnakemake

Answer 1

You need to escape braces for {4} and {6} in your shell command by doubling the brackets. Snakemake thinks they are variables of some type when they are not and hence the error.

shell:
    "umi_tools extract --extract-method=regex --bc-pattern=”(?P<umi_1>.{{6}})(?P<discard_1>.{{4}}).*” -I {input} -S {output}"