nextflow-pipelines-5a-check-genome-availability

Sub-skill of nextflow-pipelines: 5a. Check genome availability (+2).

5 stars

Best use case

nextflow-pipelines-5a-check-genome-availability is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Sub-skill of nextflow-pipelines: 5a. Check genome availability (+2).

Teams using nextflow-pipelines-5a-check-genome-availability 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

$curl -o ~/.claude/skills/5a-check-genome-availability/SKILL.md --create-dirs "https://raw.githubusercontent.com/vamseeachanta/workspace-hub/main/.agents/skills/_archive/science/bio-research/nextflow-pipelines/5a-check-genome-availability/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/5a-check-genome-availability/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How nextflow-pipelines-5a-check-genome-availability Compares

Feature / Agent	nextflow-pipelines-5a-check-genome-availability	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: 5a. Check genome availability (+2).

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

# 5a. Check genome availability (+2)

## 5a. Check genome availability


```bash
python scripts/manage_genomes.py check <genome>
# If not installed:
python scripts/manage_genomes.py download <genome>
```

Common genomes: GRCh38 (human), GRCh37 (legacy), GRCm39 (mouse), R64-1-1 (yeast), BDGP6 (fly)

## 5b. Decision points


**DECISION POINT: Confirm with user:**

1. **Genome:** Which reference to use
2. **Pipeline-specific options:**
   - **rnaseq:** aligner (star_salmon recommended, hisat2 for low memory)
   - **sarek:** tools (haplotypecaller for germline, mutect2 for somatic)
   - **atacseq:** read_length (50, 75, 100, or 150)

## 5c. Run pipeline


```bash
nextflow run nf-core/<pipeline> \
    -r <version> \
    -profile docker \
    --input samplesheet.csv \
    --outdir results \
    --genome <genome> \
    -resume
```


*See sub-skills for full details.*

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