3

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.

tedtoal
  • 1,030
  • 1
  • 10
  • 22

2 Answers2

1

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

Manavalan Gajapathy
  • 3,900
  • 2
  • 20
  • 43
0

Snakemake sees broken symlinks as missing output.

Rasmus
  • 69
  • 7