CODEWITHSUNDEEP
symlinksnakemake
tedtoal
tedtoal

Reputation: 1070

Why is Snakemake not seeing symbol link files?

I have a rule whose output files are symbolic link files. Even though the link files are being made, Snakemake exits with a MissingOutputException and lists the output files as being missing. If instead of making a symlink with "ln -s" I copy the files with "cp -p" it works. I tried increasing the --latency-wait but it made no difference.

Upvotes: 4

Views: 1173

Answers (2)

Rasmus
Rasmus

Reputation: 69

Snakemake sees broken symlinks as missing output.

Upvotes: 0

Manavalan Gajapathy
Manavalan Gajapathy

Reputation: 4089

Sounds like you are using relative path for source file when symlinking. Use absolute path.

Upvotes: 2

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