"shadow: full" mode skip symbolic links #2511
Description
Snakemake version
7.30.1
Describe the bug
Using "full" mode of shadow will skip files in symbolic link dirs
Minimal example
tree -L 1 .
> .
> ├── ref -> /abs/ref
rule UseSomeFiles:
input:
ref="ref/hg38.genome.bed",
output:
out="output/cat_output.txt"
shadow: full
shell: """
cat {input.ref} > {output.out}
"""
Excuting this will raise Error: Error: Unable to open file ref/hg38.genome.bed. Exiting.
Additional context
In job.py, os.walk automatically ignores symlink by default setting followlinks = False. https://docs.python.org/3/library/os.html#os.walk
elif self.rule.shadow_depth == "full":
snakemake_dir = os.path.join(cwd, ".snakemake")
for dirpath, dirnames, filenames in os.walk(cwd):
. . .