如何不使用Snakemake撤销更新的文件 [英] How to not rerule updated files with Snakemake

问题描述

即使已经有输出文件了，Snakemake也只想重新执行我的所有管道，因为我已经修改了第一个输出文件之一.

Even if output files are already here, Snakemake want to reexecute all of my pipeline only because I have modified one of the first output files.

我通过使用"np --reason"运行Snakemake来弄清楚:原因:输入文件被另一个作业更新:Mapping/col.sorted.bam

I figure out by running Snakemake with "np --reason": reason: Input files updated by another job: Mapping/col.sorted.bam

如何强制Snakemake不重新运行此更新文件?

How can I force Snakemake to not rerun this update file ?

谢谢

推荐答案

您可以使用选项-touch 将其标记为最新:

You can use the option --touch to mark them up to date:

-触摸，-t
触摸输出文件(将它们标记为最新，而无需真正改变他们)而不是运行他们命令.这是用来假装规则是被执行，以欺骗将来的调用蛇行.如果文件不存在则失败.

--touch, -t
Touch output files (mark them up to date without really changing them) instead of running their commands. This is used to pretend that the rules were executed, in order to fool future invocations of snakemake. Fails if a file does not yet exist.

请注意，这将触及您的所有文件，并因此修改时间戳以使其恢复原状.

Beware that this will touch all your files and thus modify the timestamps to put them back in order.

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