Skip to content

Pull requests: snakemake/snakemake

New pull request New
Clear current search query, filters, and sorts
83 Open 1,782 Closed
83 Open 1,782 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

docs: explain how to pass nested config via CLI
#3884 by kjohnsen was closed Dec 15, 2025 Loading…
2
chore(main): release 9.14.5 autorelease: tagged
#3882 by snakemake-bot was merged Dec 15, 2025 Loading…
2
fix: remove erroneous assert in the scheduler (is_main_process)
#3881 by johanneskoester was merged Dec 15, 2025 Loading…
2 tasks done
1
chore(main): release 9.14.4 autorelease: tagged
#3872 by snakemake-bot was merged Dec 9, 2025 Loading…
2
fix: fix follow-up issue with group job handling when retrieving storage
#3871 by johanneskoester was merged Dec 9, 2025 Loading…
2 tasks done
1
chore(main): release 9.14.3 autorelease: tagged
#3868 by snakemake-bot was merged Dec 8, 2025 Loading…
2
fix: ensure that queue input jobs wait if the queue is still empty upon job creation
#3866 by johanneskoester was merged Dec 7, 2025 Loading…
2 tasks done
1
2
chore(main): release 9.14.2 autorelease: tagged
#3863 by snakemake-bot was merged Dec 6, 2025 Loading…
2
fix: correctly handle groups when retrieving storage input
#3861 by johanneskoester was merged Dec 5, 2025 Loading…
2 tasks done
3
chore(main): release 9.14.1 autorelease: tagged
#3858 by snakemake-bot was merged Dec 3, 2025 Loading…
2
fix: fix issues with cyclic dependencies when using the update and before_update flag
#3857 by FelixMoelder was merged Dec 8, 2025 Loading…
2 tasks done
3
fix: ensure that spawned jobs do not handle retries themselves. The main process does that.
#3855 by johanneskoester was merged Dec 2, 2025 Loading…
2 tasks done
4
fix: always raise FileNotFoundError in case of missing files in resource expressions that do size evaluations
#3854 by johanneskoester was merged Dec 2, 2025 Loading…
2 tasks done
7
perf: retrieve storage inputs immediately before scheduling jobs instead of before running the entire workflow
#3850 by johanneskoester was merged Nov 27, 2025 Loading…
2 tasks done
5
fix: properly format input/output files in case of missing rule to produce them
#3849 by johanneskoester was merged Nov 27, 2025 Loading…
2 tasks done
2
test: Improve logging tests
#3848 by jlumpe was merged Dec 4, 2025 Loading…
27
build(deps): bump actions/checkout from 4 to 6 dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code
#3846 by dependabot bot was merged Nov 27, 2025 Loading…
1
fix: Addressed race condition in workdir_handler.py
#3844 by matthewakram was merged Nov 27, 2025 Loading…
2 tasks done
2
fix: cleanup update-marked output files of failed jobs if there was no backup to restore them
#3843 by johanneskoester was merged Nov 27, 2025 Loading…
2 tasks done
6
fix: mount local storage prefix into containers
#3840 by johanneskoester was merged Nov 27, 2025 Loading…
2 tasks done
14
fix: fix backup for output marked by update
#3839 by FelixMoelder was merged Nov 19, 2025 Loading…
2 tasks
3
chore(main): release 9.14.0 autorelease: tagged
#3835 by snakemake-bot was merged Nov 27, 2025 Loading…
2
chore(main): release 9.13.7 autorelease: tagged
#3834 by snakemake-bot was merged Nov 7, 2025 Loading…
2
fix: backup output files marked for update and restore them in case of job failures
#3833 by johanneskoester was merged Nov 7, 2025 Loading…
2 tasks done
9
fix: correct Windows callable path handling
#3832 by Eric-Nitschke was merged Nov 27, 2025 Loading…
2 tasks done
1
2
ProTip! Follow long discussions with comments:>50.