Proper way to include wrappers with absolute paths?

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Issue #1300 wontfix
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I want to include wrappers from my local file system in the wrapper of my rule. For this, I'm using file:// URLs.

Snakemake now warns me as follows:

File path file:///fulll/path/to/environment.yaml contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.

Am I doing something wrong?

Snakemake version is 5.6.0.

Comments (2)

  1. Johannes Köster

    Hi,
    it looks like you entered that URL for a conda env, not for the wrapper directive. The wrapper directive accepts file URLs (as stated in the docs). The conda env does not. The reason is that it is only needed for locally defined environments. For your wrapper, snakemake will automatically pick the environment.yaml that is defined in the wrapper directory (even if it is a local wrapper declared via a file URL.

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