# Nextflow Pipelines Generate Automatically

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

- Skill: `vamseeachanta/nextflow-pipelines-generate-automatically` (Agent Skill)
- Install (CLI): `npx skillmds@latest add vamseeachanta/nextflow-pipelines-generate-automatically`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vamseeachanta/nextflow-pipelines-generate-automatically/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Research & Search
- Author: vamseeachanta (https://skillmd.com/u/vamseeachanta)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/vamseeachanta/nextflow-pipelines-generate-automatically

---


# 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.*