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[docs] Update usage permissions #380

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34 changes: 19 additions & 15 deletions USAGE.md
Original file line number Diff line number Diff line change
Expand Up @@ -121,53 +121,55 @@ $ tw compute-envs import --name=my_aws_ce_v1 ./my_aws_ce_v1.json

## Pipelines

A Pipeline is composed of a workflow repository, launch parameters, and a Compute Environment. Pipelines are used to define frequently used pre-configured workflows in a Workspace.
A pipeline consists of a workflow repository, launch parameters, and a Compute Environment. Pipelines are used to define pre-configured workflows in a Workspace.

### Adding a Pipeline

Add a pre-configured Pipeline to the Launchpad that can be re-used later:
Add a pre-configured pipeline to the Launchpad that can be re-used later:

```console
$ tw pipelines add --name=my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params.yaml https://github.com/nextflow-io/rnaseq-nf

New pipeline 'my_rnaseq_nf_pipeline' added at user workspace
```

The `--params-file` option was used to pass a set of default parameters that will be associated with the Pipeline in the Launchpad.
The `--params-file` option was used to pass a set of default parameters that will be associated with the pipeline in the Launchpad.

> **NOTE**: The `params-file` option should be a YAML or JSON file.

### Importing/exporting a Pipeline
### Importing/exporting a pipeline

It is possible to export the configuration details for a Pipeline in JSON format for scripting and reproducibility purposes.
You can export the configuration details of a pipeline in JSON format for scripting and reproducibility purposes.

```console
$ tw pipelines export --name=my_rnaseq_nf_pipeline my_rnaseq_nf_pipeline_v1.json

Pipeline exported into 'my_rnaseq_nf_pipeline_v1.json'
```

Similarly, a Pipeline can easily be imported into a Workspace from a previously exported JSON file.
Similarly, a pipeline can easily be imported into a Workspace from a previously exported JSON file.

```console
$ tw pipelines import --name=my_rnaseq_nf_pipeline_v1 ./my_rnaseq_nf_pipeline_v1.json

New pipeline 'my_rnaseq_nf_pipeline_v1' added at user workspace
```

### Updating a Pipeline
### Updating a pipeline

The default launch parameters can be changed using the `update` command:

```console
tw pipelines update --name=my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params_2.yaml
```

## Launching Pipelines
## Launching pipelines

### Launching a preconfigured Pipeline
### Launching a preconfigured pipeline

When launching a Pipeline from the Launchpad, if no custom parameters are passed via the CLI then the defaults set for the Pipeline in the Launchpad will be used.
When launching a pipeline from the Launchpad, if no custom parameters are passed via the CLI then the defaults set for the pipeline in the Launchpad will be used.

> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launch users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines.

```console
$ tw launch my_rnaseq_nf_pipeline
Expand All @@ -184,9 +186,9 @@ When using `--wait`, `tw` can exit with one of two exit codes:

> **TIP**: Use `--wait=SUCCEEDED` if you want the command to wait until the Pipeline execution is complete.

### Launching a Pipeline with custom parameters
### Launching a pipeline with custom parameters

Launch the Pipeline with different parameters
To launch the pipeline with different parameters:

```console
$ tw launch my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params_2.yaml
Expand All @@ -196,9 +198,9 @@ $ tw launch my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params_2.y
https://tower.nf/user/abhinav/watch/2XDXxX0vCX8xhx
```

### Launching any Pipeline
### Launching any pipeline

It is also possible to directly launch Pipelines that have not been explicitly added to the Launchpad in a Tower Workspace by using the full Pipeline repository URL:
Platform CLI can directly launch pipelines that have not been explicitly added to the Launchpad in a platform workspace by using the full pipeline repository URL:

```console
$ tw launch https://github.com/nf-core/rnaseq --params-file=./custom_rnaseq_params.yaml --compute-env=my_aws_ce --revision 3.8.1 --profile=test,docker
Expand All @@ -208,11 +210,13 @@ $ tw launch https://github.com/nf-core/rnaseq --params-file=./custom_rnaseq_para
https://tower.nf/user/abhinav/watch/2XDXxX0vCX8xhx
```

> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launch users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines.

In the above command:

- Pipeline level parameters are defined within the `custom_rnaseq_params.yaml` file
- Other parameters such as `--profile` and `--revision` can also be specified
- A non-primary Compute Environment has been used to launch the Pipeline
- A non-primary Compute Environment has been used to launch the pipeline

## Workspaces

Expand Down
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