REANA-Workflow-Engine-Snakemake 0.9.3

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

• progress: handle stopped jobs (#78) (4829d80)

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)

REANA-Workflow-Engine-Snakemake 0.9.2

• 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.

REANA-Workflow-Engine-Snakemake 0.9.1

• 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.

REANA-Workflow-Engine-Snakemake 0.9.0

• 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.

REANA-Workflow-Engine-Snakemake 0.8.1

• Adds support for specifying kubernetes_job_timeout for Kubernetes compute backend jobs.
• Adds polling job-controller to determine job statuses instead of checking files.

REANA-Workflow-Engine-Snakemake 0.8.0

• Adds initial REANA Snakemake executor implementation.
• Adds support for snakemake reports generation.
• Adds support for REANA custom resources.
• Adds support for parallel job execution.