fix!: make star index output and star align input idx a multiext()

[dlaehnemann]

The motivation for explicitly naming the outputs of star indexing and the inputs for star align, are to be able to use input.size_mb for dynamic memory requirements for star align (and possibly star index).

QC

• I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• Bug Fixes

  • Improved validation and clearer error messages for genome index inputs
  • More reliable determination of the genome directory used by STAR workflows

• Performance / Reliability

  • Per-step resource estimation added (memory and thread usage) to improve scheduling and stability

• Documentation / Metadata

  • Tool display name updated to "STAR align" and authorship list extended

• Tests

  • Updated tests to reflect expanded genome index outputs

[coderabbitai]

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 02c1287f-ef7b-4e4c-b4cf-a2545f068f7e

📥 Commits

Reviewing files that changed from the base of the PR and between 62fb88e and 4580989.

📒 Files selected for processing (1)

• test_wrappers.py

📝 Walkthrough

Walkthrough

Rules and wrappers for STAR index and alignment now enumerate index files with multiext(), add per-rule threads and resources.mem_mb calculations, and compute --genomeDir via os.path.commonpath() (wrappers). Tests and module metadata were adjusted accordingly.

Changes

Cohort / File(s)	Summary
STAR align rules & wrapper bio/star/align/test/Snakefile, bio/star/align/wrapper.py, bio/star/align/meta.yaml	input.idx changed from a single directory string to multiext() listing STAR index files; threads: 8 moved into rules and resources.mem_mb added (computed as input.size_mb + threads * 150); wrapper derives genome_dir = os.path.commonpath(...), raises explicit KeyError if input.idx missing, and uses --genomeDir {genome_dir}. meta.yaml name updated and an author added.
STAR index rules & wrapper bio/star/index/test/Snakefile, bio/star/index/wrapper.py, bio/star/index/meta.yaml	output changed from directory("{genome}") to multiext("{genome}/", ...) enumerating STAR index files; log moved/added and resources.mem_mb added (lambda using input.size_mb); wrapper computes genome_dir = os.path.commonpath(snakemake.output) and adds --limitGenomeGenerateRAM with mem_bytes derived from snakemake.resources.mem_mb. An author was added in meta.yaml.
Tests test_wrappers.py	test_star_index updated to invoke bio/star/index wrapper with explicit list of expected index output files instead of a single directory target.

Sequence Diagram(s)

mermaid
sequenceDiagram
participant Snakemake
participant Wrapper as "Wrapper (bio/star/*/wrapper.py)"
participant FS as "Filesystem (index files)"
participant STAR as "STAR CLI"
Snakemake->>Wrapper: provide inputs (multiext index files), params, resources
Wrapper->>FS: compute genome_dir = os.path.commonpath(inputs/outputs)
Wrapper->>Wrapper: compute mem_bytes from snakemake.resources.mem_mb
Wrapper->>STAR: invoke CLI with --genomeDir=genome_dir and --limitGenomeGenerateRAM=mem_bytes
STAR->>FS: read/write index files
STAR-->>Snakemake: exit status/logs

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and specifically describes the main change: converting STAR index output and align input from simple strings to multiext() expressions for better file dependency tracking.
Description check	✅ Passed	The description explains the motivation, includes the required QC checklist with all items checked, and confirms adherence to contribution guidelines.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/make-star-index-output-multiexp

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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 `@bio/star/align/wrapper.py`:
- Around line 48-55: The call to path.commonpath(snakemake.input.get("idx")) can
raise ValueError when "idx" is missing, so first retrieve
snakemake.input.get("idx") into a local (e.g., idx = snakemake.input.get("idx"))
and guard it for None/empty; if missing, raise the intended KeyError; otherwise
call path.commonpath(idx) and wrap that call in a try/except ValueError to
convert any ValueError into the same KeyError message. Update the block around
genome_dir, path.commonpath and the KeyError so missing or invalid idx always
results in the custom KeyError.

🪄 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: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 307c58b5-994e-4fc3-b0dd-ceeb309bd836

📥 Commits

Reviewing files that changed from the base of the PR and between 3fb92b0 and 340b974.

📒 Files selected for processing (5)

• bio/star/align/test/Snakefile
• bio/star/align/wrapper.py
• bio/star/index/test/Snakefile
• bio/star/index/wrapper.py
• test_wrappers.py

[dlaehnemann]

Note: with the new output / input structure for the star index, this will break previously copy-pasted versions of the two wrappers. So this is marked as breaking and a major version bump. So if there are other breaking changes coming up, maybe this could be bundled. And we could possibly wait for other non-breaking stuff to be released, before merging this PR here. It is not urgent,

[fgvieira]

Looks good!

[dlaehnemann]

Do you have any other breaking changes coming up? Or should we just merge and release this, bumping to a new major version?