nextflow-pipelines-step-2-select-pipeline
Sub-skill of nextflow-pipelines: Step 2: Select Pipeline.
Best use case
nextflow-pipelines-step-2-select-pipeline is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Sub-skill of nextflow-pipelines: Step 2: Select Pipeline.
Teams using nextflow-pipelines-step-2-select-pipeline should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/step-2-select-pipeline/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How nextflow-pipelines-step-2-select-pipeline Compares
| Feature / Agent | nextflow-pipelines-step-2-select-pipeline | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Sub-skill of nextflow-pipelines: Step 2: Select Pipeline.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# Step 2: Select Pipeline ## Step 2: Select Pipeline **DECISION POINT: Confirm with user before proceeding.** | Data Type | Pipeline | Version | Goal | |-----------|----------|---------|------| | RNA-seq | `rnaseq` | 3.22.2 | Gene expression | | WGS/WES | `sarek` | 3.7.1 | Variant calling | | ATAC-seq | `atacseq` | 2.1.2 | Chromatin accessibility | Auto-detect from data: ```bash python scripts/detect_data_type.py /path/to/data ``` For pipeline-specific details: - [references/pipelines/rnaseq.md](references/pipelines/rnaseq.md) - [references/pipelines/sarek.md](references/pipelines/sarek.md) - [references/pipelines/atacseq.md](references/pipelines/atacseq.md) ---
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