nextflow-development

Files (22)

• LICENSE.txt
• SKILL.md
• geo-sra-acquisition.md · references/
• installation.md · references/
• atacseq.md · references/pipelines/
• rnaseq.md · references/pipelines/
• sarek.md · references/pipelines/
• troubleshooting.md · references/
• check_environment.py · scripts/
• genomes.yaml · scripts/config/
• atacseq.yaml · scripts/config/pipelines/
• rnaseq.yaml · scripts/config/pipelines/
• sarek.yaml · scripts/config/pipelines/
• detect_data_type.py · scripts/
• generate_samplesheet.py · scripts/
• manage_genomes.py · scripts/
• sra_geo_fetch.py · scripts/
• __init__.py · scripts/utils/
• file_discovery.py · scripts/utils/
• ncbi_utils.py · scripts/utils/
• sample_inference.py · scripts/utils/
• validators.py · scripts/utils/

SKILL.md (first lines)

# nf-core Pipeline Deployment

Run nf-core bioinformatics pipelines on local or public sequencing data.

**Target users:** Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis.

## Workflow Checklist

```
- [ ] Step 0: Acquire data (if from GEO/SRA)
- [ ] Step 1: Environment check (MUST pass)
- [ ] Step 2: Select pipeline (confirm with user)
- [ ] Step 3: Run test profile (MUST pass)
- [ ] Step 4: Create samplesheet
- [ ] Step 5: Configure & run (confirm genome with user)
- [ ] Step 6: Verify outputs
```

---

## Step 0: Acquire Data (GEO/SRA Only)

**Skip this step if user has local FASTQ files.**

For public datasets, fetch from GEO/SRA first. See [references/geo-sra-acquisition.md](references/geo-sra-acquisition.md) for the full workflow.

**Quick start:**

```bash
# 1. Get study info
python scripts/sra_geo_fetch.py info GSE110004

# 2. Download (interactive mode)
python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i

# 3. Generate samplesheet
python scripts/sra_geo_fetch.py samplesheet GSE110004 --fastq-dir ./fastq -o samplesheet.csv
```

**DECISION POINT:** After fetching study info, confirm with user:
- Which sample subset to download (if multiple data types)
- Suggested genome and pipeline

Then continue to Step 1.

---

## Step 1: Environment Check

**Run first. Pipeline will fail without passing environment.**

```bash
python scripts/check_environment.py
```

All critical checks must pass. If any fail, provide fix instructions:

### Docker issues

| Problem | Fix |
|---------|-----|
| Not installed | Install from https://docs.docker.com/get-docker/ |
| Permission denied | `sudo usermod -aG docker $USER` then re-login |
| Daemon not running | `sudo systemctl start docker` |

### Nextflow issues

| Problem | Fix |
|---------|-----|
| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
| Version < 23.04 | `nextflow self-update` |

### Java issues

| Problem | Fix |
|---------|-----|
| Not installed / < 11 | `sudo apt install openjdk-11-jdk` |

**Do not proceed until all checks pass.** For HPC/Singularity, see [references/troubleshooting.md](references/troubleshooting.md).

---

## 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)

---

## Step 3: Run Test Profile

**Validates environment with small data. MUST pass before real data.**

```bash
nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output
```

| Pipeline | Command |
|----------|---------|
| rnaseq | `nextflow run nf-core/rnaseq -r 3.22.2 -profile test,docker --outdir test_rnaseq` |
| sarek | `nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek` |
| atacseq | `nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq` |

Verify:

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