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I am running a snakemake pipeline on a couple of files that I symlinked from another directory.

However, it seems that the snakemake file does not recognize the input files when they are symlinked. Is this supposed to happen, or is there someway around this? I am getting a 'missing input files' error.

When I cp my input file into the exact same directory and run the script, it works fine. It's not a big deal to have to cp stuff around, but with a ton of data this might be a little more trouble than it's worth.

Version is 4.6.0

dddxxx
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  • You will have to provide more details http://snakemake.readthedocs.io/en/stable/project_info/faq.html#can-the-input-of-a-rule-be-a-symlink – Foldager Apr 12 '18 at 19:43

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