New modules: STAR Suite alignment and genome generation
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- Dominant language
- Nextflow
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Description
I plan to contribute two related modules for
STAR Suite 1.7.1:
starsuite/genomegeneratebuilds a STAR Suite index and can include the
transcriptome FASTA required by TranscriptVB;starsuite/alignprovides 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.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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