Sub-skill of nextflow-pipelines: Generate automatically (+2).
Scanned 9/9/2026
Install to Claude Code
Skills Directorynpx -y skills add vamseeachanta/workspace-hub --skill generate-automatically --agent claude-codeInstalls into .claude/skills of the current project.
Are you the author of Generate Automatically?
Add the live security badge to your README — it updates automatically with every re-scan.
[](https://www.skillsdirectory.com/skills/vamseeachanta-generate-automatically)More formats (shields.io, HTML) on the badges page.
---
name: nextflow-pipelines-generate-automatically
description: 'Sub-skill of nextflow-pipelines: Generate automatically (+2).'
version: 1.0.0
category: science
type: reference
scripts_exempt: true
---
# 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.*
Is this your skill, or is something wrong with this listing? Request removal or report an issue. Author removals are honored within 72 hours.
No comments yet. Be the first to comment!
