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junjun-zhang authored Jun 25, 2020
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Expand Up @@ -32,26 +32,26 @@ which specific version of a module is to be imported.

To run the pipeline, please follow instruction [here](https://www.nextflow.io/docs/latest/getstarted.html#installation) to install Nextflow (version `20.01.0` or higher) first.

Run `1.0.0` version of the pipeline:
Run `1.3.0` version of the pipeline:
```
nextflow run icgc-argo/dna-seq-processing-wfs -r 1.0.0 -params-file <your_params_file.json>
nextflow run icgc-argo/dna-seq-processing-wfs -r 1.3.0 -params-file <your_params_file.json>
```

You may need to run `nextflow pull icgc-argo/dna-seq-processing-wfs` if the version `1.0.0` is new since last time the pipeline was run.
You may need to run `nextflow pull icgc-argo/dna-seq-processing-wfs` if the version `1.3.0` is new since last time the pipeline was run.

Please note that SONG/SCORE services need to be available and you have appropriate API token.

## Testing

Automated Travis CI testing has been set up. However, tests will be skipped when CI is triggered on a Travis server due to reliance on SONG/SCORE services which are not available. A possible solution is to spin up
SONG/SCORE services running use Docker at Travis, this will require some work but should be doable. Before this
is resolved, we can run tests locally (where we have access to SONG/SCORE services) with the following commands under the root
directory of this Git repository:
Automated Travis CI testing has been set up. However, tests relying on SONG/SCORE will be skipped when CI is triggered
on a Travis server where SONG/SCORE services are not available. When running tests locally (where SONG/SCORE services may be
available) please use the following commands under the root directory of this Git repository:

```
# perform all tests when SONG/SCORE is available
export api_token=<your_api_token>
pytest -v
# or perform test without using SONG/SCORE
# or perform tests that do not need SONG/SCORE
TRAVIS=true pytest -v
```

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