> ## 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 init

> CLI reference for the primerlab init command

Generate a template configuration file.

## Synopsis

```bash theme={null}
primerlab init [options]
```

## Options

| Option       | Short | Description                             |
| ------------ | ----- | --------------------------------------- |
| `--workflow` | `-w`  | Workflow type: pcr, qpcr (default: pcr) |
| `--output`   | `-o`  | Output filename (default: config.yaml)  |

## Examples

### Generate PCR Config

```bash theme={null}
primerlab init
# Creates config.yaml
```

### Generate qPCR Config

```bash theme={null}
primerlab init --workflow qpcr --output my_qpcr.yaml
```

## Generated Config

The generated config includes all available options with comments:

```yaml theme={null}
workflow: pcr

input:
  sequence: "YOUR_SEQUENCE_HERE"
  # Or use: sequence_path: "input.fasta"

parameters:
  primer_size: {min: 18, opt: 20, max: 24}
  tm: {min: 58.0, opt: 60.0, max: 62.0}
  product_size_range: [[200, 600]]
  gc: {min: 40, max: 60}

output:
  directory: "output_pcr"
```