nf-core / nf-core/modules

New modules: STAR Suite alignment and genome generation

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Nextflow
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Description

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

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the proposed starsuite/genomegenerate and starsuite/align entry points, then review their Dockerfiles and the module tests described in the issue. Verify the existing nf-core/tools and nf-test checks, including paired-end, single-end, TranscriptVB, and missing-transcriptome cases. Done means both modules lint cleanly and all stated Docker and Singularity tests pass.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker
Domain
bioinformatics, testing-qa
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
35/100

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