Include pharokka -> phold with plot

[Ulthran]

No description provided.

[Copilot]

Pull Request Overview

This PR adds integration of Pharokka and Phold (with plotting) into the sbx_induceome workflow.

• Replace standalone PHOLD GBK output with a plotted PNG in the all_induceome rule
• Introduce install, annotation, and run rules for Pharokka and Phold, plus a new induceome_phold_plot rule
• Update configuration (pharokka_db) and documentation (README badge and config entry)

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
sbx_induceome.smk	Updated all_induceome to expect PNG outputs; added rules for installing Pharokka/Phold DBs, running Pharokka, and plotting Phold results
config.yml	Added pharokka_db configuration key
README.md	Fixed Tests badge URL and documented pharokka_db

Comments suppressed due to low confidence (5)

sbx_induceome.smk:67

• The pipeline’s all_induceome rule no longer includes the Pharokka output, so the new induceome_pharokka step won’t run when invoking all. Consider adding an expand(INDUCEOME_FP / "pharokka" / "{sample}_pharokka.gbk", sample=SBX_INDUCEOME_SAMPLES) entry.

expand(INDUCEOME_FP / "phold" / "{sample}_plot" / "phold.png",

README.md:23

• Typo: pharokka_dp should be pharokka_db to match the key in config.yml.

-  - pharokka_dp: Path to the pharokka db (full path to the directory that will hold db files)

sbx_induceome.smk:247

• [nitpick] New induceome_pharokka rule is added but there are no tests covering this step. Consider adding tests to verify Pharokka annotation output.

rule induceome_pharokka:

sbx_induceome.smk:321

• [nitpick] New induceome_phold_plot rule is introduced without corresponding tests. Adding a test to ensure plots are generated correctly would improve reliability.

rule induceome_phold_plot:

sbx_induceome.smk:224

• [nitpick] The multiline path expression for output.pharokka is split across lines without parentheses, which may lead to syntax errors. Consider wrapping the entire expression in parentheses or placing it on a single line.

pharokka=Path(Cfg["sbx_induceome"]["pharokka_db"])