Add STAR Suite alignment and genome generation modules

[lhhunghimself]

Description

Closes #12825.

Adds two container-only modules for STAR Suite:

• starsuite/genomegenerate builds a STAR Suite genome index and can include the
  transcriptome required by TranscriptVB.
• starsuite/align performs STAR alignment and optionally integrated TranscriptVB
  transcript/gene quantification.

STAR Suite 1.7.1 extends upstream STAR 2.7.11b and is MIT-licensed. The modules
use the existing multi-architecture Biodepot release image pinned by OCI digest:

docker.io/biodepot/star-suite@sha256:0ced4e4941b8a7347c1583598381e6abe25d798df09759c59ede0e6c6dc4e1d3

There is deliberately no Conda environment. Each module includes the Dockerfile
required for software not distributed through Bioconda, and Conda/Mamba profiles
fail with a clear message. This keeps the nf-core component on the same artefact
built and versioned by STAR Suite's existing Biodepot CI/CD pipeline.

The two components are intentionally submitted together because the alignment
tests build their small TranscriptVB-capable reference with
starsuite/genomegenerate.

Container review requested: the current implementation intentionally uses
the project-maintained Biodepot image pinned by immutable digest. Please confirm
whether this reference is acceptable or whether the release must be mirrored
under quay.io/nf-core; I will update the PR if a mirror is required.

The alignment module remains generic: without quantification arguments it behaves
as an alignment-only STAR replacement. TranscriptVB outputs are Salmon-compatible
quant.sf files and an additional results directory suitable for tximport.

Testing

• nf-core/tools 4.1.0: both module lints pass with no warnings or failures.
• nf-test 0.9.5 / Nextflow 25.10.2: 8/8 real and stub tests pass with Docker.
• nf-test 0.9.5 / Nextflow 25.10.4: 8/8 pass with Singularity.
• Paired-end, single-end, alignment-only, sorted BAM, unmapped reads,
  transcriptome indexing and missing-transcriptome failure are covered.
• nf-core modules lint starsuite/align: 56 passed, no warnings/failures.
• nf-core modules lint starsuite/genomegenerate: 54 passed, no warnings/failures.
• Both Dockerfiles build successfully.

Citation

Hung LH, Baker D, Flynn B, Huangfu D, Luo R, Robson P, Zhou T, Yeung KY. STAR
Suite: an open-source single-executable transcriptomics engine for reproducible,
AI agent-assisted processing. bioRxiv. 2026.
https://doi.org/10.64898/2026.03.09.710580

Checklist

• This comment describes the change and its motivation.
• Tests cover the new code and failure modes.
• The modules follow the contribution conventions and naming rules.
• No new test-data repository files are required.
• No TODO statements remain in the submitted components.
• STAR Suite and upstream STAR versions are broadcast to topic: versions.
• Inputs, outputs, ext.args, ext.prefix and resource labels follow the
  module specifications.
• Dockerfiles are included because STAR Suite is not on Bioconda.
• Docker tests pass.
• Singularity tests pass.
• Conda testing is not applicable; the modules fail early with an explicit
  container-runtime requirement.
• Resolve the disclosed container-review question and apply any required
  quay.io/nf-core mirror before merge.