Working.md

# Working with BiTIA CLI
BiTIA has three commands to work on it:
- run
- submit
- logs

### Bitia run can be employed in following ways:

#### 1. Running commands

```bash
$ bitia run "samtools run foo.fa#http://example.com/foo.fa"
```
- TO BE FILLED


#### 2. Running Pipelines

```bash
$ bitia run pipeline.sh
```
- TO BE FILLED