nextflow-implementor

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Nextflow Implementor Skill

Nextflow 开发者技能

Read and follow agent-conduct and nextflow-conventions before starting.

开始前请阅读并遵循agent-conduct和nextflow-conventions规范。

TDD Cycle

TDD 循环

For each acceptance test, follow every step:

Write a failing nf-test in
```
modules/local/<tool>/tests/main.nf.test
```
.

Run:

nf-test test modules/local/<tool>/tests/main.nf.test

Write minimal process/workflow to pass.
Ensure the process emits
```
versions.yml
```
with tool version(s).
Verify container is specified (prefer nf-core module, then Seqera Wave / BioContainers, then Docker Hub).
Run:
```
nf-core pipelines lint
```
and fix issues.
Re-run nf-test to confirm it passes.

针对每个验收测试，请遵循以下所有步骤：

在
```
modules/local/<tool>/tests/main.nf.test
```
中编写一个会失败的nf-test测试用例。

运行：

nf-test test modules/local/<tool>/tests/main.nf.test

编写最小化的流程/工作流以通过测试。
确保流程输出包含工具版本信息的
```
versions.yml
```
文件。
确认已指定容器（优先使用nf-core模块，其次是Seqera Wave / BioContainers，最后是Docker Hub）。
运行：
```
nf-core pipelines lint
```
并修复问题。
重新运行nf-test以确认测试通过。

Module-per-Function Rule

单功能单模块规则

Split each tool/function into its own module under

modules/local/<tool>/main.nf

with a corresponding

tests/main.nf.test

. One process per file, one test file per module.

将每个工具/功能拆分为独立模块，存放在

modules/local/<tool>/main.nf

，并对应编写

tests/main.nf.test

测试文件。每个文件对应一个流程，每个模块对应一个测试文件。

nf-core Module Re-use

复用nf-core模块

Before creating a local module, check nf-core:

bash

nf-core modules list remote | grep <tool>

If a suitable module exists, install it (

nf-core modules install <tool>

) instead of writing a local one. Only create local modules when no nf-core module covers the requirement.

在创建本地模块前，请先检查nf-core：

bash

nf-core modules list remote | grep <tool>

如果存在合适的模块，使用

nf-core modules install <tool>

安装它，而非编写本地模块。仅当没有nf-core模块满足需求时，才创建本地模块。

Container Discovery

容器查找

For local modules without nf-core equivalents, find open-source containers:

Search https://seqera.io/wave/ for the tool.
Search https://biocontainers.pro/.
Fall back to Docker Hub / Quay.io official images.

Specify both docker and singularity container paths.

对于没有对应nf-core模块的本地模块，查找开源容器的步骤：

在https://seqera.io/wave/搜索该工具。
在https://biocontainers.pro/搜索。
最后选择Docker Hub / Quay.io的官方镜像。

同时指定docker和singularity的容器路径。

Workflow

工作流

Implement ONE item at a time: write nf-tests for the spec.md acceptance tests, then write implementation to make them pass, strictly following the TDD cycle above. Consult spec.md for full details.

After all modules pass, ensure:

```
nextflow.config
```
has default params.
```
conf/base.config
```
has resource labels.
```
conf/modules.config
```
has publishDir directives.
Profiles work:
```
docker
```
,
```
singularity
```
,
```
test
```
.
All versions collected into final
```
versions.yml
```
.
```
docs/usage.md
```
and
```
docs/output.md
```
are written for end-users.

一次实现一个任务：为spec.md中的验收测试编写nf-tests用例，然后编写实现代码使其通过测试，严格遵循上述TDD循环。详细信息请参考spec.md。

所有模块测试通过后，请确保：

```
nextflow.config
```
包含默认参数。
```
conf/base.config
```
包含资源标签。
```
conf/modules.config
```
包含publishDir指令。
配置文件正常工作：
```
docker
```
、
```
singularity
```
、
```
test
```
。
所有版本信息已收集到最终的
```
versions.yml
```
中。
已为终端用户编写
```
docs/usage.md
```
和
```
docs/output.md
```
文档。