REANA-Workflow-Engine-Snakemake

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REANA-Workflow-Engine-Snakemake is a component of the REANA reusable and reproducible research data analysis platform. It takes care of instantiating, executing and managing Snakemake based computational workflows.

Features

  • start Snakemake workflows

  • control workflow steps

Usage

The detailed information on how to install and use REANA can be found in docs.reana.io.

Changelog

0.9.3 (2024-03-04)

Build

  • docker: install correct extras of reana-commons submodule (#79) (fd9b88a)

  • docker: non-editable submodules in “latest” mode (#73) (c3595c2)

  • python: bump all required packages as of 2024-03-04 (#85) (66e81e2)

  • python: bump shared REANA packages as of 2024-03-04 (#85) (d07f91f)

Features

  • config: get max number of parallel jobs from env vars (#84) (69cfad4)

  • executor: upgrade to Snakemake v7.32.4 (#81) (4a3f359)

Bug fixes

Code refactoring

  • docs: move from reST to Markdown (#82) (31de94f)

Continuous integration

  • commitlint: addition of commit message linter (#74) (145b7e7)

  • commitlint: allow release commit style (#86) (fd032db)

  • commitlint: check for the presence of concrete PR number (#80) (b677913)

  • release-please: initial configuration (#74) (9b16bd0)

  • release-please: update version in Dockerfile (#77) (3c35a67)

  • shellcheck: fix exit code propagation (#80) (ad15c0d)

Documentation

  • authors: complete list of contributors (#83) (4782678)

0.9.2 (2023-12-12)

  • Adds automated container image building for amd64 architecture.

  • Adds metadata labels to Dockerfile.

  • Fixes creation of image thumbnails for output files in Snakemake HTML execution reports.

  • Fixes container image building on the arm64 architecture.

0.9.1 (2023-09-27)

  • Changes remote storage file support to use XRootD 5.6.0.

  • Fixes the reported total number of jobs for restarted workflows by excluding cached jobs that were simply reused from previous runs in the workspace and not really executed by Snakemake.

  • Fixes an issue where workflows could get stuck waiting for already-finished jobs.

  • Fixes container image names to be Podman-compatible.

0.9.0 (2023-01-19)

  • Adds support for specifying slurm_partition and slurm_time for Slurm compute backend jobs.

  • Adds support for XRootD remote file locations in workflow specification definitions.

  • Adds support for Kerberos authentication for workflow orchestration.

  • Adds support for Rucio authentication for workflow jobs.

  • Changes global setting of maximum number of parallel jobs to 300.

  • Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies.

  • Fixes progress reporting for failed workflow jobs.

0.8.1 (2022-02-07)

  • Adds support for specifying kubernetes_job_timeout for Kubernetes compute backend jobs.

  • Adds polling job-controller to determine job statuses instead of checking files.

0.8.0 (2021-11-22)

  • Adds initial REANA Snakemake executor implementation.

  • Adds support for snakemake reports generation.

  • Adds support for REANA custom resources.

  • Adds support for parallel job execution.

Contributing

Bug reports, issues, feature requests, and other contributions are welcome. If you find a demonstrable problem that is caused by the REANA code, please:

  1. Search for already reported problems.

  2. Check if the issue has been fixed or is still reproducible on the latest master branch.

  3. Create an issue, ideally with a test case.

If you create a pull request fixing a bug or implementing a feature, you can run the tests to ensure that everything is operating correctly:

$ ./run-tests.sh

Each pull request should preserve or increase code coverage.

License

MIT License

Copyright (C) 2021, 2022, 2023, 2024 CERN.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

In applying this license, CERN does not waive the privileges and immunities granted to it by virtue of its status as an Intergovernmental Organization or submit itself to any jurisdiction.

Authors

The list of contributors in alphabetical order: