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New modules: STAR Suite alignment and genome generation #12825

Description

@lhhunghimself

I plan to contribute two related modules for
STAR Suite 1.7.1:

  • starsuite/genomegenerate builds a STAR Suite index and can include the
    transcriptome FASTA required by TranscriptVB;
  • starsuite/align provides generic STAR-compatible alignment with optional
    integrated TranscriptVB transcript and gene quantification.

The components are proposed together because the alignment module's tests use
starsuite/genomegenerate to construct a small, TranscriptVB-capable reference
fixture. The alignment module otherwise remains generic: without TranscriptVB
arguments it behaves as an alignment-only STAR replacement.

STAR Suite 1.7.1 is MIT-licensed, reports upstream STAR 2.7.11b and retains
genome-index compatibility 2.7.4a. It is not currently distributed by Bioconda.
The proposed modules use the public multi-architecture Biodepot release image,
pinned to OCI digest
sha256:0ced4e4941b8a7347c1583598381e6abe25d798df09759c59ede0e6c6dc4e1d3,
and include the required Dockerfiles. The associated component PR explicitly
asks reviewers whether that immutable reference can remain canonical or should
be mirrored to quay.io/nf-core. A core-team request will be made only if the
review directs us to do so.

Local verification is complete with nf-core/tools 4.1.0, nf-test 0.9.5 and
Nextflow 25.10.2/25.10.4:

  • both module lints pass with no warnings or failures;
  • all 8 real/stub tests pass with Docker and Singularity;
  • paired-end, single-end, alignment-only, sorted BAM, unmapped FASTQ,
    transcriptome generation and a missing-transcriptome failure are covered.

Planned first consumer: an opt-in --aligner starsuite route in nf-core/rnaseq.

Preprint: https://doi.org/10.64898/2026.03.09.710580

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