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| Format: | Recurso digital |
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Zenodo
2020
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| Online-Zugang: | https://doi.org/10.5281/zenodo.16420882 |
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- <h1>PALANTIR-WORKFLOWS</h1> <p><a href="https://github.com/broadinstitute/palantir-workflows/actions/workflows/run_tests.yaml/badge.svg?branch=main"></a> <a href="https://github.com/broadinstitute/palantir-workflows/actions/workflows/test_dockerfiles.yaml/badge.svg?branch=main"></a></p> <p>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 <a href="https://app.terra.bio/">Terra</a> through <a href="https://dockstore.org/">Dockstore</a>.</p> <p><strong>Remember, this is a public repository, so anything you put in this repo is publicly viewable.</strong></p> <h2>Testing Workflows</h2> <p>Automated WDL testing is implemented using <a href="https://github.com/rickymagner/watt">watt</a>. To add tests, update <a href="test/watt_config.yml">test/watt_config.yml</a>. See the watt documentation for usage details. Tests are run using github actions, controlled by <a href=".github/workflows/run_tests.yaml">.github/workflows/run_tests.yaml</a>. Automated testing also validates all WDLs found in the repository, regardless of whether tests have been added for the particular WDL, using <code>womtool validate</code>. Automated testing is performed on all PR's, as well as any pushes to the <code>main</code> branch.</p> <p>During testing, WDLs are run on GCP, with the execution bucket <code>gs://palantir-workflows-test-execution</code>. Generally, input and expected output files are stored in <code>gs://palantir-workflows-test-data</code>. The stdout from watt will be visible in the github actions UI, and cromwell log files can be found in a zipped artifact named <code>cromwell_logs</code>, also in the github actions UI.</p> <h2>Using the Dockstore Github App to Automatically Update Workflows in Dockstore/Terra</h2> <p>Workflows registered in Dockstore can be automatically synced when changes are pushed to this repo by adding their information to <code>.dockstore.yml</code>. 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 <a href="https://docs.dockstore.org/en/develop/getting-started/github-apps/github-apps.html">documentation</a>.</p>