> ## 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 batch-run

> CLI reference for the primerlab batch-run command

Run multiple primer designs in batch mode.

## Synopsis

```bash theme={null}
primerlab batch-run [options]
```

## Options

| Option                | Short | Description                                     |
| --------------------- | ----- | ----------------------------------------------- |
| `--configs`           | `-c`  | Directory with configs OR comma-separated paths |
| `--fasta`             | `-f`  | Multi-FASTA file with multiple sequences        |
| `--config`            |       | Shared config for multi-FASTA mode              |
| `--output`            | `-o`  | Output directory (default: ./batch\_output)     |
| `--export`            | `-e`  | Export format for summary (default: xlsx)       |
| `--continue-on-error` |       | Continue if some designs fail                   |

## Modes

### Mode 1: Multiple Config Files

```bash theme={null}
# From directory
primerlab batch-run --configs ./configs/ --output ./results/

# From specific files
primerlab batch-run --configs config1.yaml,config2.yaml --output ./results/
```

### Mode 2: Multi-FASTA with Shared Config

```bash theme={null}
primerlab batch-run --fasta genes.fasta --config shared.yaml --output ./results/
```

## Examples

### Batch from Directory

```bash theme={null}
primerlab batch-run \
  --configs ./project_configs/ \
  --output ./batch_results/ \
  --continue-on-error
```

### Multi-FASTA Mode

```bash theme={null}
primerlab batch-run \
  --fasta examples/multi_sequences.fasta \
  --config examples/pcr_standard.yaml \
  --output ./batch_results/
```

## Output

* Individual results per sequence
* `batch_summary.xlsx` - Combined Excel summary
* Console summary with success/fail stats