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Add tests for --is_private flag for different kinds of data

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#80 0 comentarios 0 reacciones 0 asignados Ver en GitHub

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Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
55/100
Tipo de issue
Nueva funcionalidad
Claridad
Bastante claro
Estado de actividad
Tranquilo
Área
testing-qa

Línea de trabajo

Comienza con la sección Data privacy de docs/usage.md y después examina los conf/test_.config existentes, las hojas de ejemplo y los patrones de tests/.nf.test para reads, ensamblajes metagenómicos y MAGs/bins. Pregunta a un mantenedor por accessions privadas de Webin adecuadas antes de crear las pruebas. El trabajo está terminado cuando cada tipo de datos cubre datos de origen privados con --is_private y el caso de fallo documentado sin él.

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

Descripción

enhancement

Difficulty: Easy

Why this matters: ENA (European Nucleotide Archive) lets you build a submission on top of data that isn't public yet, as long as your Webin account has access to it. The pipeline supports this through --is_private. There's currently no automated test covering this for any of the three submission types (reads, metagenomic assemblies, MAGs/bins), so a bug in this part of the pipeline could slip through unnoticed.

Some terms: ENA (European Nucleotide Archive) is the public repository this pipeline submits data to. Webin is ENA's account and authentication system, you need a Webin account to submit anything, and registration is free and self-service. "Private data" means data that has been submitted to ENA but isn't publicly visible yet, only accessible to the Webin account that submitted it (or one it's been shared with). docs/usage.md has a "Data privacy" section with a table of the different combinations (public/private source data, public/private submission) and which flags each one needs, that table is the best starting point.

Skills / experience: nf-test: creation and running of tests (see the nf-core nf-test testing guide if this is new to you).

Suggested approach:

  1. Read the "Data privacy" section of docs/usage.md closely, this is the main reference for what --is_private does and when it's needed.
  2. For each of the three data types (reads, metagenomic assemblies, MAGs/bins), add a test that references private source data with --is_private set. No need to also test private vs public submission visibility, just focus on getting private source data covered for all three types.
  3. ** ⭐ You'll need actual private test data already submitted under a Webin test account for this, check with a maintainer whether suitable private accessions already exist, or if you need to submit some first.**
  4. Add a conf/test_*.config per data type and a sample sheet that uses registered private accessions, following the pattern of the existing ones.
  5. Add a matching tests/*.nf.test per data type.
  6. Also worth testing the failure case: private source data referenced without --is_private should fail, as described in the docs table.
Lenguaje dominante
Nextflow
Estrellas
22
Forks
11
Merge medio
1 d 4 h
PR fusionados (30 d)
8

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