Support submission of metagenomic assemblies generated from co-assemblies
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评估
- 难度
- 4/5
- 预计耗时
- 3-5 天
- 新手友好度
- 35/100
- Issue 类型
- 功能
- 描述清晰度
- 基本清楚
- 活跃度
- 停滞
- 领域
- data
调研方向
阅读 docs/usage.md 的 metagenomic_assemblies 部分，然后查看 PR #66，并检查其描述以了解剩余工作。调查多次运行时的 CoverM 输出及其覆盖率计算，必要时使用 nf-test。完成的标准是 co-assembly 提交流程已通过测试，并且 PR #66 已完成审查并合并。
由索引模型根据 Issue 内容生成。
描述
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:
- Read the
metagenomic_assembliesmode section ofdocs/usage.mdto be familiar with submission process. - Check out the PR #66 branch and read its description, which already lists what's left to do.
- Fix the coverage calculation bug it flags (the multi-run CoverM output has more columns than the single-run case handles).
- Help get the PR reviewed and merged.
- 主要语言
- Nextflow
- 星标
- 22
- 派生
- 11
- 平均合并
- 1 天 4 小时
- 30 天内合并 PR
- 8
环境准备
在浏览器里用你自己的 GitHub 账号启动这个项目的开发容器。
- 没有 Dockerfile 或 Docker Compose 文件
- 有 Pull Request 模板
- 阅读贡献指南
从这里开始
- 先读完整个 Issue，再读项目的贡献指南。
- 在 Issue 下留言说明你要接手 —— 这能避免两个人做同样的事。
- Fork 仓库，在一个分支上完成修改。
- 提交 Pull Request，并在描述里引用这个 Issue 编号。
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