Refactor: Extract software version collection boilerplate into shared function

[cmkobel]

Summary

The pattern for writing software version info to .software_version.txt is copy-pasted across 25+ shell blocks in rule files (sample_annotation.smk, sample_advanced_annotation.smk, batch_advanced_annotation.smk, batch_quality_control.smk, batch_phylogeny.smk, etc.).

A typical instance looks like:

echo -e "tool_name\t$(tool --version)" > "$(dirname {output})/.software_version.txt"

Similarly, the database version collection pattern (echo -e "$(date -Iseconds)\t$(dirname {input.database_representative})"...) appears in ~6 places.

Proposed approach

Extract a shared shell function (or Snakemake wrapper/macro) that takes the tool name, version command, and output path. This would:

• Reduce duplication across rule files
• Prevent bugs when one copy is updated but others aren't
• Make it easier to change the version reporting format globally

Files to touch

• workflow/rules/sample_annotation.smk (lines ~139, 181–182)
• workflow/rules/sample_advanced_annotation.smk (lines ~20–21, 56, 107–110, 184–185, 296–299)
• workflow/rules/batch_advanced_annotation.smk (lines ~15–16, 57–61)
• workflow/rules/batch_quality_control.smk (lines ~42, 44–45)
• workflow/rules/batch_phylogeny.smk (lines ~18, 47, 58–61, 81, 115, 150)
• Plus others — grep for .software_version.txt to find all instances

[cmkobel]

After investigating this, the software version collection commands are too diverse to meaningfully abstract — each tool has a completely different way of reporting its version (--version, -v, piping through grep, special workarounds like fasttree). The only shared part is the output path pattern $(dirname {output.X})/.software_version.txt, which is a single line per rule.

The database version pattern (6 occurrences) IS uniform:

echo -e "$(date -Iseconds)\t$(dirname {input.database_representative})" > "$(dirname {output.X})/.database_version.txt"

However, Snakemake's shell block formatting makes it difficult to define reusable shell functions (braces conflict with format parsing). A wrapper script would work but adds indirection for a one-liner.

Recommendation: Close this issue or downgrade to low priority. The pattern is repetitive but each instance is a self-contained single line — abstracting it would add complexity without real readability gains.