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palantir-workflows

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Utility workflows for the DSP hydro.gen team (formerly palantir)

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# PALANTIR-WORKFLOWS

[![Test Status](https://github.com/broadinstitute/palantir-workflows/actions/workflows/run_tests.yaml/badge.svg?branch=main)](https://github.com/broadinstitute/palantir-workflows/actions/workflows/run_tests.yaml/badge.svg?branch=main) [![Dockerfiles Status](https://github.com/broadinstitute/palantir-workflows/actions/workflows/test_dockerfiles.yaml/badge.svg?branch=main)](https://github.com/broadinstitute/palantir-workflows/actions/workflows/test_dockerfiles.yaml/badge.svg?branch=main)

Utility workflows used by the DSP's Palantir team.  This repository should be used to manage frequently used utility workflows for the team, and facilitate their use on [Terra](https://app.terra.bio/) through [Dockstore](https://dockstore.org/).

**Remember, this is a public repository, so anything you put in this repo is publicly viewable.**

## Testing Workflows

Automated WDL testing is implemented using [watt](https://github.com/rickymagner/watt).
To add tests, update  [test/watt_config.yml](test/watt_config.yml).
See the watt documentation for usage details.  Tests are run using github actions, controlled by [.github/workflows/run_tests.yaml](.github/workflows/run_tests.yaml).  Automated testing also validates all WDLs found in the repository, regardless of whether tests have been added for the particular WDL, using `womtool validate`.  Automated testing is performed on all PR's, as well as any pushes to the `main` branch.

During testing, WDLs are run on GCP, with the execution bucket `gs://palantir-workflows-test-execution`.  Generally, input and expected output files are stored in `gs://palantir-workflows-test-data`.  The stdout from watt will be visible in the github actions UI, and cromwell log files can be found in a zipped artifact named `cromwell_logs`, also in the github actions UI.

## Using the Dockstore Github App to Automatically Update Workflows in Dockstore/Terra
Workflows registered in Dockstore can be automatically synced when changes are pushed to this repo by adding their information to `.dockstore.yml`. 
In this way, a change pushed to a branch in this repo can be automatically propagated into any Terra workspaces using the workflow. 
Details can be found at Dockstore's Github App [documentation](https://docs.dockstore.org/en/develop/getting-started/github-apps/github-apps.html).

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