cromwell-cli

README

Cromwell CLI

---

This program was created to:

• Facilitate the installation and configuration of a Cromwell Server with a local backend using Docker.
• Provide the functionality to reuse already processed jobs by default, via the Call Cache mechanism.
• Provide ways to interact with the server, such as submitting, querying, and inspecting jobs.
• Familiarize myself with the Go language.

The Broad Institute has its own CLI, be sure to check it out.

But don't forget to give us a star if ours has been helpful 😉

Quickstart

You can download the binary from the releases page for your platform or install it by running the following command:

curl https://raw.githubusercontent.com/lmtani/cromwell-cli/main/install.sh | bash

It's allowed to install the binary in any location, but you will need to set variable PREFIX when running the install script.

curl https://raw.githubusercontent.com/lmtani/cromwell-cli/main/install.sh | PREFIX=/home/taniguti/bin bash

This way you don't need to provide privileged access.

Features

• Start Cromwell Server locally
• List workflows by name
• Submit a workflow
• Abort a workflow
• Navigate through workflow metadata
• Get metadata
• Get outputs
• Get inputs
• Make requests to a remote Cromwell Server protected by IAP (Google Identity Aware Proxy)
• For Google Cloud backend jobs: estimate resource usage
• Have a cool name

Examples

Local server deploy

You need to open a new terminal after starting the server. Press CTRL+c when you want to shut it down.

Submit workflow

Query workflows

Navigate through workflow metadata

Cromwell behind Google Identity Aware Proxy

This is a very specific use case, but it's here. If you are using a Cromwell server behind Google Identity Aware Proxy (IAP), you can use the --iap flag to make requests to it. You will need to provide the expected audience of the token, which is the client_id of your oauth. For example:

You will also need to set the GOOGLE_APPLICATION_CREDENTIALS environment variable to the path of your Google service account JSON file.

GOOGLE_APPLICATION_CREDENTIALS=/path/to/your/google/service-account.json
HOST="https://your-cromwell.dev"
AUDIENCE="Expected audience"
cromwell-cli --host "${HOST}" --iap "${AUDIENCE}" query