vep download cache vs vep annotate

[lczech]

Snakemake version snakemake-wrappers: 0.74.0

Describe the bug The vep download cache wrapper uses the vep_install --AUTO cf mode, which downloads the cache and fasta data. However, the vep annotate wrapper expects that the cache directory has exactly one subdirectory, and hence fails when the cache was downloaded with the wrapper.

Proposed solution Use --AUTO c instead.

In feature request issue 366, I have furthermore posted a suggestion for a feature where I also added a more flexible solution for this bug. The relevant part:

# Get a param from the config that defaults to c, that is, download the cache only,
# but can be changed by the user to also download fasta by providing `automode: cf` in the config.
# This would trigger the single-subdirectory check in the vep annotate wrapper though.
automode = snakemake.params.get("automode", "c")

shell(
    "vep_install --AUTO {automode} "
    ...
)

[github-actions[bot]]

This issue was marked as stale because it has been open for 6 months with no activity.