# Collapsing First Pass v1.8.1

## Version of tools in docker image (/container/Dockerfile)

| Tool            | Version | Location                                                                             |
| --------------- | ------- | ------------------------------------------------------------------------------------ |
| java base image | 8       | -                                                                                    |
| Marianas        | 1.8.1   | <https://github.com/juberpatel/Marianas/releases/download/v1.8.1/Marianas-1.8.1.jar> |

## CWL

* CWL specification 1.0
* Use example\_inputs.yaml to see the inputs to the cwl
* Example Command using [toil](https://toil.readthedocs.io):

```bash
    > toil-cwl-runner marianas_first_pass.cwl example_inputs.yaml
```
