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Pull requests: snakemake/snakemake

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Pull requests list

chore(main): release 9.23.1 autorelease: pending
#4227 opened Jun 11, 2026 by snakemake-bot Contributor Loading…
2
fix: workaround SSL unsafe legacy renegotiation error when generating report (closes #2027)
#4221 opened Jun 7, 2026 by botbikamordehai2-sketch Loading…
1
6
fix: failure when module-specific <pathvar> in input func of a rules.final.input statement in main Snakefile
#4218 opened Jun 5, 2026 by dlaehnemann Member Loading…
2 of 7 tasks
2
fix: complete RunArgs refactoring, add various testcases
#4209 opened May 31, 2026 by jiangyun-fun Loading…
@johanneskoester
17
feat: added post-deploy.sh support for --containerize
#4206 opened May 27, 2026 by maarten-k Contributor Loading…
3 tasks done
1
5
fix: add test for #4197
#4199 opened May 21, 2026 by fgvieira Contributor Loading…
3 of 7 tasks
1
feat: allow users to define a shell wrapper around all shell directives
#4185 opened May 6, 2026 by LukaP-BB Loading…
3 tasks done
7
fix: scoped module container directive
#4184 opened May 5, 2026 by twillis209 Loading…
6 of 7 tasks
1
4
feat: add ability to deploy workflow runtime and plugin dependencies on the fly WIP Work in progress. Not meant for merging.
#4182 opened May 5, 2026 by johanneskoester Contributor Loading…
2 of 7 tasks
14
refactor: Remove Python < 3.11 compat
#4167 opened Apr 24, 2026 by ulgens Contributor Loading…
1 of 3 tasks
7
chore: prepare for internal Rust modules by migrating to maturin as build backend (draft)
#4165 opened Apr 22, 2026 by seneschall Contributor • Draft
7 tasks
1
feat: Add new feature to support external perl scripts (solves #4162)
#4164 opened Apr 21, 2026 by b-brankovics Contributor Loading…
3 of 7 tasks
1
26
feat: Add --no-apptainer-check flag with tests and documentation
#4157 opened Apr 17, 2026 by tinyheero Contributor Loading…
7 tasks done
1
fix: cannot drop ruleinfo of a and use rule a as b in module if use b from module
#4148 opened Apr 11, 2026 by Hocnonsense Contributor Loading…
6 of 7 tasks
2
@Hocnonsense
10
feat: allow Snakemake to discover all required checkpoints in a single evaluation
#4125 opened Mar 20, 2026 by Hocnonsense Contributor Loading…
6 of 7 tasks
2
@Hocnonsense
21
feat!: file://relative in wrapper: now resolves relative to the directory…
#4118 opened Mar 18, 2026 by Hocnonsense Contributor Loading…
4 of 7 tasks
@Hocnonsense
7
test: module override
#4110 opened Mar 17, 2026 by fgvieira Contributor Loading…
2 of 7 tasks
1
feat: add support for quarto in script directive enhancement New feature or request WIP Work in progress. Not meant for merging.
#4101 opened Mar 13, 2026 by GaspardR Contributor • Draft
1 of 7 tasks
1
4
test: Add testcase for mixed conda and container workflow
#4100 opened Mar 13, 2026 by LKress Contributor Loading…
2 of 7 tasks
1
fix(checkpoints): Fix importing checkpoints into modules bug Something isn't working
#4097 opened Mar 13, 2026 by jonasfreimuth Contributor Loading…
3 of 7 tasks
1
@johanneskoester @Hocnonsense
10
chore: add .pre-commit-config.yaml
#4094 opened Mar 13, 2026 by tedil Contributor Loading…
1 of 3 tasks
2
feat: add tolerance and impatient params to optional input
#4086 opened Mar 13, 2026 by CameronMcClymont Loading…
1 of 2 tasks
27
docs: Add faq section on resource definition priorization
#4081 opened Mar 13, 2026 by LKress Contributor Loading…
1 of 2 tasks
9
feat: add --share-benchmark flag to send benchmark telemetry to a remote collector enhancement New feature or request
#4078 opened Mar 12, 2026 by btraven00 Member • Draft
2 tasks done
12
feat: Support remote snakefile in CLI and API
#4077 opened Mar 12, 2026 by clelange Contributor Loading…
2 tasks done
40
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