Refactor: Deduplicate download rules in downloads.smk

[cmkobel]

Summary

workflow/rules/downloads.smk contains 7 download rules that all follow the same conditional structure:

if [ -f "{output}" ]; then
    touch {output:q}
else
    # Download logic (unique per tool)
    touch {output:q}
fi

The boilerplate around the actual download command is identical in every rule.

Proposed approach

Consider a helper function or template that wraps the "skip if exists, otherwise download and touch" logic, so each rule only needs to specify its unique download command. This would reduce repetition and make it easier to add new download rules consistently.

Files to touch

• workflow/rules/downloads.smk (rules at approximately lines 6, 43, 85, 142, 179, 214, 245)

[cmkobel]

After investigating this, the download commands within each rule are complex multi-line shell scripts with tool-specific logic (wget + tar, tool-specific downloaders like bakta_db download, dbcan_build, etc.). They can't be passed to a simple wrapper function.

The if/else boilerplate per rule is ~7 lines, and while it's repeated 7 times, each rule's unique download logic is 5-15 lines. A wrapper script would need to accept arbitrary shell commands as arguments, which is fragile.

Additionally, the if [ -f "{output}" ] check may be redundant — Snakemake already skips rules whose outputs exist. But removing it could introduce edge-case issues, so it's a defensive pattern worth keeping.

Recommendation: Close this issue or downgrade to low priority.