nextflow-pipelines-generate-automatically

Sub-skill of nextflow-pipelines: Generate automatically (+2).

5 stars

Best use case

nextflow-pipelines-generate-automatically is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Sub-skill of nextflow-pipelines: Generate automatically (+2).

Teams using nextflow-pipelines-generate-automatically 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/generate-automatically/SKILL.md --create-dirs "https://raw.githubusercontent.com/vamseeachanta/workspace-hub/main/.agents/skills/_archive/science/bio-research/nextflow-pipelines/generate-automatically/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/generate-automatically/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How nextflow-pipelines-generate-automatically Compares

Feature / Agent	nextflow-pipelines-generate-automatically	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: Generate automatically (+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

# Generate automatically (+2)

## Generate automatically


```bash
python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv
```

The script:
- Discovers FASTQ/BAM/CRAM files
- Pairs R1/R2 reads
- Infers sample metadata
- Validates before writing

**For sarek:** Script prompts for tumor/normal status if not auto-detected.

## Validate existing samplesheet


```bash
python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>
```

## Samplesheet formats


**rnaseq:**
```csv
sample,fastq_1,fastq_2,strandedness
SAMPLE1,/abs/path/R1.fq.gz,/abs/path/R2.fq.gz,auto
```

**sarek:**
```csv
patient,sample,lane,fastq_1,fastq_2,status
patient1,tumor,L001,/abs/path/tumor_R1.fq.gz,/abs/path/tumor_R2.fq.gz,1

*See sub-skills for full details.*

Related Skills

nextflow-pipelines

from vamseeachanta/workspace-hub

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data for gene expression, variant calling, and chromatin accessibility analyses.