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Support submission of metagenomic assemblies generated from co-assemblies

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  • ¿Algo no está bien?
#61 1 comentario 0 reacciones 1 asignado Ver en GitHub

Los mantenedores suelen responder en 1 día

@ochkalova ya está trabajando en esto.

Desde el 15/10/2026.

  • #66 de @ochkalova — abierto

Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
35/100
Tipo de issue
Nueva funcionalidad
Claridad
Bastante claro
Estado de actividad
Estancado
Área
data

Línea de trabajo

Lee la sección metagenomic_assemblies de docs/usage.md, luego revisa PR #66 y comprueba en su descripción cuál es el trabajo pendiente. Investiga la salida de CoverM en múltiples ejecuciones y su cálculo de cobertura, usando nf-test cuando sea necesario. Se considera terminado cuando el flujo de envío de co-assembly esté probado y PR #66 haya sido revisado y fusionado.

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

Descripción

assembly_submit enhancement

Difficulty: Medium

Why this matters: the pipeline submits metagenomic assemblies to ENA (European Nucleotide Archive). A co-assembly is when reads from several sequencing runs are assembled together into one set of contigs, instead of assembling each run on its own. This is common in metagenomics because it can improve results for organisms that are rare in any single sample. Right now the metagenomic_assemblies mode assumes one run per assembly, so there's no way to describe "this assembly came from runs A, B and C together". This is the other half of the co-assembly problem, on the metagenomic assemblies side (see issue # for the equivalent problem on the MAGs/bins side).

Good to know before starting: there's already an open pull request (#66) that implements most of this, it accepts semicolon-separated run accessions and read files, calculates coverage across multiple runs, and registers a stand-in sample that ties the co-assembly back to all its source runs. The task here is to pick that PR up and finish it rather than start from scratch.

Some terms: ENA (European Nucleotide Archive) is the public repository this pipeline submits data to, and Webin is ENA's account and authentication system needed to submit anything (free, self-service registration). Co-assembly is explained above. An "umbrella" or virtual sample is a synthetic ENA sample used to represent data that comes from more than one original sample, since ENA submissions need to point at exactly one sample.

Skills / experience: Nextflow, reading and continuing someone else's in-progress code, nf-test (see the nf-core nf-test testing guide if this is new to you). Familiarity with the concept of genome coverage depth would be helpful.

Suggested approach:

  1. Read the metagenomic_assemblies mode section of docs/usage.md to be familiar with submission process.
  2. Check out the PR #66 branch and read its description, which already lists what's left to do.
  3. Fix the coverage calculation bug it flags (the multi-run CoverM output has more columns than the single-run case handles).
  4. Help get the PR reviewed and merged.
Lenguaje dominante
Nextflow
Estrellas
22
Forks
11
Merge medio
1 d 4 h
PR fusionados (30 d)
8

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Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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