feat: various changes to accomodate new wf catalog features

[m-jahn]

• this PR implements some changes with regard to two new features in the wf catalog which I'll try to advertise a bit more in the future:
  • tube maps will be built as long as there is .test subdir which supports running a test case (snakemake -c 1 -d .test --forceall --rulegraph)
  • there's no longer a need to have manually curated table of wf params in the README. As long as the wf has a config.schema.y(a)ml file, this will be used to render a table automatically
• example: here or here
• the idea is to have as little manual curation as possible for workflow docs and automate the most
• other minor formatting changes and updates, closes bump superlinter verison in github actions workflow to v8 #25

Summary by CodeRabbit

• New Features

  • Added defaults and stricter types/required fields for key workflow configuration parameters.

• Documentation

  • Updated README with workflow diagram and parameter table note.
  • Streamlined configuration docs by removing the separate Parameters section.

• Dependencies

  • Bumped tool versions for FastQC and MultiQC; updated CI action versions.

• Chores

  • Updated license year range.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

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📥 Commits

Reviewing files that changed from the base of the PR and between dbadc80 and 5835ce7.

📒 Files selected for processing (2)

• .github/workflows/conventional-prs.yaml
• .github/workflows/main.yaml

✅ Files skipped from review due to trivial changes (2)

• .github/workflows/conventional-prs.yaml
• .github/workflows/main.yaml

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📝 Walkthrough

Walkthrough

Updates include a license year range bump, small README edits, removal of a parameters table from config docs, repositioning of a Snakemake default_target, rule tweaks and tool version bumps, and an expanded config JSON-schema with added types, defaults, and required fields.

Changes

Cohort / File(s)	Summary
Documentation & License LICENSE, README.md, config/README.md	Updated LICENSE copyright span to 2021-2026; added one sentence to README.md Usage about workflow diagram and parameter table; removed the standalone "Parameters" section from config/README.md.
Snakemake top-level workflow/Snakefile	Moved default_target: True out of the input: block to be a direct key under rule all.
Snakemake rules workflow/rules/process_reads.smk	Reordered log/message placements across several rules; replaced shell backtick extraction with params.output_prefix for simulate_reads and updated DWGSIM invocation; moved fastqc threads: 1 into rule header; bumped tool wrapper versions (fastqc v6.0.0→v7.6.0, multiqc v6.0.0→v8.1.1).
Configuration schema workflow/schemas/config.schema.yaml	Added type: object at root; updated sample_sheet description and default (config/samples.tsv); added default "" and required status for get_genome.ncbi_ftp; changed simulate_reads.read_length/read_number from number→integer, added defaults (100, 10000) and marked them required; expanded top-level required to include get_genome and simulate_reads.
CI workflows .github/workflows/main.yaml, .github/workflows/conventional-prs.yaml	Bumped GitHub Action major versions: actions/checkout@v4→@v6 and super-linter v7→v8 in main.yaml; updated amannn/action-semantic-pull-request v5→v6 in conventional-prs.yaml.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Possibly related PRs

• fix: recommended .yaml file extension, latest schema version #19: Directly related to schema updates in workflow/schemas/config.schema.yaml.

Poem

🐰 The license hops forward, years in tow,
Docs trimmed neat where old tables used to show,
Rules shuffle logs and tools get new shoes,
Schema counts numbers with integer pews,
I nibble a carrot and sigh—workflows grow.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title is vague and overly generic; 'various changes' and 'accommodate new wf catalog features' lack specificity about what was actually changed.	Consider a more specific title that describes the main change, such as 'refactor: prepare workflow for catalog schema-based documentation' or 'feat: add config schema support for auto-generated parameter tables'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@workflow/schemas/config.schema.yaml`:
- Around line 15-18: The schema currently sets a required field
get_genome.ncbi_ftp with default: "" which makes an empty-but-present value
possible; remove the empty default (delete default: "") and instead add a
non-empty constraint (e.g., minLength: 1 or a URI/hostname pattern) for property
ncbi_ftp so the validator rejects blank values; update any docs/examples rather
than changing requiredness, and ensure the consumer in process_reads.smk (the
wget usage) will only receive a validated, non-empty URL.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 49921d3a-d7eb-4c43-b462-a5dd4c45e143

📥 Commits

Reviewing files that changed from the base of the PR and between edc3127 and dbadc80.

📒 Files selected for processing (6)

• LICENSE
• README.md
• config/README.md
• workflow/Snakefile
• workflow/rules/process_reads.smk
• workflow/schemas/config.schema.yaml

💤 Files with no reviewable changes (1)

• config/README.md

[dlaehnemann]

Nice. I didn't know about these features, but appreciate them.

One additional thing to maybe add, would be extensive comments in the config/config.yaml file itself. But this could also be done in a separate pull request. This is where I usually put information on the kinds of values each setting can have.