> ## Documentation Index
> Fetch the complete documentation index at: https://primerlab-genomic.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

# primerlab run

> CLI reference for the primerlab run command

Run a primer design workflow.

## Synopsis

```bash theme={null}
primerlab run <workflow> [options]
```

## Arguments

| Argument   | Required | Description                               |
| ---------- | -------- | ----------------------------------------- |
| `workflow` | Yes      | Workflow type: `pcr`, `qpcr`, or `crispr` |

## Options

| Option            | Short | Description                           |
| ----------------- | ----- | ------------------------------------- |
| `--config`        | `-c`  | Path to configuration YAML file       |
| `--out`           | `-o`  | Override output directory             |
| `--debug`         |       | Enable debug logging                  |
| `--dry-run`       |       | Validate config without running       |
| `--export`        | `-e`  | Export formats (comma-separated)      |
| `--mask`          | `-m`  | Region masking mode                   |
| `--quiet`         | `-q`  | Suppress warnings (v0.1.6)            |
| `--validate`      | `-V`  | Run in-silico PCR validation (v0.2.3) |
| `--blast`         |       | Run off-target check (v0.3.1)         |
| `--blast-db`      |       | Path to BLAST database                |
| `--report`        | `-R`  | Generate enhanced report (v0.3.3)     |
| `--report-format` |       | Report format: markdown, html, json   |
| `--report-output` |       | Report output path                    |

## Examples

### Basic PCR Design

```bash theme={null}
primerlab run pcr --config my_pcr.yaml
```

### qPCR with TaqMan Probe

```bash theme={null}
primerlab run qpcr --config my_qpcr.yaml
```

### With Masking

```bash theme={null}
# Auto-detect lowercase and N-masked regions
primerlab run pcr --config my_pcr.yaml --mask auto
```

### Export to Multiple Formats

```bash theme={null}
primerlab run pcr --config my_pcr.yaml --export idt,benchling
```

### Quiet Mode (v0.1.6)

```bash theme={null}
# Suppress warnings for scripted pipelines
primerlab run pcr --config my_pcr.yaml --quiet
```

### Dry Run

```bash theme={null}
# Validate config without running
primerlab run pcr --config my_pcr.yaml --dry-run
```

### With In-silico Validation (v0.2.3)

```bash theme={null}
# Design + validate primers against template
primerlab run pcr --config my_pcr.yaml --validate
```

### With BLAST Off-target Check (v0.3.1)

```bash theme={null}
# Design + check off-targets
primerlab run pcr --config my_pcr.yaml --blast --blast-db genome.fasta
```

### With Report Generation (v0.3.3)

```bash theme={null}
# Generate enhanced HTML report
primerlab run pcr --config my_pcr.yaml --report --report-format html --report-output report.html
```

## Mask Modes

| Mode        | Description                                  |
| ----------- | -------------------------------------------- |
| `auto`      | Detect both lowercase and N-masked regions   |
| `lowercase` | Only detect lowercase (RepeatMasker) regions |
| `n`         | Only detect N-masked regions                 |
| `none`      | No masking (default)                         |

## Export Formats

| Format      | Description          |
| ----------- | -------------------- |
| `idt`       | IDT ordering format  |
| `sigma`     | Sigma-Aldrich format |
| `thermo`    | Thermo Fisher format |
| `benchling` | Benchling CSV import |
| `xlsx`      | Excel spreadsheet    |