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Add eukaryotic MAGs/bins support

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#40 0 comentarios 0 reacciones 1 asignado Ver en GitHub

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@KateSakharova ya está trabajando en esto.

Desde el 13/10/2026.

Evaluación

Dificultad
5/5
Tiempo estimado
Más de una semana
Aptitud para principiantes
35/100
Tipo de issue
Nueva funcionalidad
Claridad
Bastante claro
Estado de actividad
Estancado
Área
bioinformatics

Línea de trabajo

Empieza leyendo las limitaciones de mags y bins en docs/usage.md y, después, sigue la integración de CheckM2 en workflows/genomesubmit.nf. Revisa los módulos nf-core disponibles y define cómo se identifican los genomas como eucariotas. Se considerará terminado cuando las comprobaciones de calidad y de RNA para eucariotas funcionen con cobertura de nf-test y la documentación refleje las limitaciones actualizadas.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

enhancement eukaryotes

Difficulty: Hard

Why this matters: the pipeline submits MAGs and bins to ENA (European Nucleotide Archive). Right now, if you don't already know the completeness, contamination and RNA presence of your genome, the pipeline calculates them for you, but only for prokaryotes (using CheckM2, barrnap and tRNAScan). If your MAG or bin is eukaryotic, those tools don't apply, so today you can only submit eukaryotic genomes if you provide all that metadata yourself in the samplesheet.

Some terms: ENA (European Nucleotide Archive) is the public repository this pipeline submits data to. A MAG (metagenome assembled genome) or bin is a genome reconstructed from metagenomic sequencing data. Completeness and contamination are quality scores based on how many expected marker genes are found. CheckM2 calculates these for prokaryotes, BUSCO or EukCC are the equivalent widely used tools for eukaryotes. RNA presence refers to detecting rRNA/tRNA genes, currently done with tools built for prokaryotes too.

Skills / experience: comfortable writing or adapting a Nextflow module (there's likely already a BUSCO/EukCC module in nf-core/modules to reuse rather than write from scratch) and workflows, some familiarity with genome annotation/analysis tools is helpful but not required going in. If Nextflow pipeline tests are new to you, the nf-core nf-test testing guide is worth a look since you'll need to add test coverage too.

Suggested approach:

  1. Read the mags and bins modes section of docs/usage.md, especially the "Limitations" part, to see exactly what's missing for eukaryotic genomes today.
  2. Read through workflows/genomesubmit.nf to see how CheckM2 is currently wired in.
  3. Pick one piece to start with rather than everything at once, BUSCO/EukCC for completeness/contamination is a reasonable first target.
  4. Install BUSCO/EukCC nf-core/module using nf-core toolkit.
  5. You'll need some way to flag a genome as eukaryotic so the workflow knows to route it to BUSCO/EukCC instead of CheckM2, there isn't a column for that yet, so part of the task is deciding how to add one (new samplesheet column, or a pipeline parameter).
  6. Automate BUSCO database creation/download if it is required.
  7. Once this is done, configure barrnap and tRNAScan to detect eukaryotic genes (see their documentation to find exact flags). If it's impossible explore other tools that can be used for the purpose.
  8. Add nf-test coverage using a small eukaryotic test genome.
  9. Update the limitations section in docs/usage.md once this is working.
Lenguaje dominante
Nextflow
Estrellas
22
Forks
11
Merge medio
1 d 4 h
PR fusionados (30 d)
8

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