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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
18 stars 19 forks source link

feat: cancel workflow#127 #139

Closed cmeesters closed 1 month ago

cmeesters commented 2 months ago

adds the --slurm-cancel-workflow-upon-failure flag, which allows cancelling the entire workflows upon job failure, superseeds --keep-going.

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago

Walkthrough

The changes involve the reorganization of Snakemake documentation regarding executor behavior, specifically the handling of job failures. A new boolean attribute, cancel_workflow_upon_failure, has been added to the ExecutorSettings class, affecting workflow cancellation based on job success. Additionally, the documentation now includes information about the --keep-going and --slurm-cancel-workflow-upon-failure flags, enhancing user options for managing job failures.

Changes

Files Change Summary
docs/further.md Reorganized content on executor behavior; added details on job failure handling and new flags for workflow management.
snakemake_executor_plugin_slurm/init.py Introduced cancel_workflow_upon_failure attribute in ExecutorSettings class; modified job checking logic accordingly.

Possibly related PRs

Poem

In the meadow, hopping free,
Changes come, oh joy for me!
With flags to guide my little way,
I’ll dance through jobs both night and day.
If one should fail, I’ll still be spry,
For workflows now can wave goodbye! 🐇✨

[!TIP]

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cmeesters commented 2 months ago

ok, cool - this PR successfully completes all tests. Ready to merge? @johanneskoester

johanneskoester commented 1 month ago

This does not really make sense as a function inside an executor. Instead, it makes sense as a flag for Snakemake itself, next to --keep-going, and can be implemented in an executor agnostic way.

johanneskoester commented 1 month ago

The place to add this would be snakemake/scheduler.py in there error handling method there.