Sapporo test workflow

This repository summarizes examples and results of actual widely used workflows executed with Sapporo and Yevis.

The workflows that were verified are as follows:

• broadinstitute/gatk/MitochondriaPipeline
• nf-core/rnaseq
• biosciencedbc/jga-analysis - per-sample workflow

Verification environment

• Ubuntu: 20.04
• Docker: 20.10.15
• sapporo-service: 1.2.3
• yevis-cli: 0.3.3

Execution methods and results

We use Yevis as the execution runner for Sapporo. Yevis reads a file called yevis-metadata, which describes workflow metadata and test execution methods, and generates a workflow execution request to Sapporo. (i.e., a POST request to /runs in Sapporo) Therefore, as execution methods, we have prepared execution commands using Yevis and yevis-metadata files.

In addition, as execution results, we uploaded run_dir, the result of Sapporo's execution, to Zenodo. The run_dir contains various workflow provenances such as input/output files, execution logs, and run requests.

broadinstitute/gatk/MitochondriaPipeline

The execution method is as below:

yevis test https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_gatk-workflows_mitochondria-pipeline.yml

The execution results are uploaded to .

nf-core/rnaseq

The execution method is as below:

yevis test https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_nf-core_rnaseq.yml

The execution results are uploaded to .

biosciencedbc/jga-analysis - per-sample workflow

The execution method is as below:

yevis test https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_jga-workflow_per-sample.yml

The execution results are uploaded to .

License

Apache-2.0. See the LICENSE.