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John Major
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first pass at mods for pcluster-slurm
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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<!--Note the Snakemake version and the plugin version for which you experience the bug.
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Note the SLURM version, too. You can get the versions with:
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$ snakemake --version
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$ mamba list | grep "snakemake-executor-plugin-slurm"
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$ mamba list | grep "snakemake-executor-plugin-pcluster-slurm"
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$ sinfo --version
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Please only report bugs of the **latest stable release of Snakemake and this plugin**.
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If possible please check whether the bug has been already fixed in the main branch.-->

‎.github/workflows/release-please.yml‎

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id: release
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with:
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release-type: python
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package-name: snakemake-executor-plugin-slurm
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package-name: snakemake-executor-plugin-pcluster-slurm
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2020
publish:
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runs-on: ubuntu-latest

‎CHANGELOG.md‎

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# Changelog
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## [0.11.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.10.2...v0.11.0) (2024-09-27)
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### Features
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* added requeue option to client ([#136](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/136)) ([b0ff160](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/b0ff160533536e2d82f738ad6e9e1a268ba616cb))
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## [0.10.2](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.10.1...v0.10.2) (2024-09-11)
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### Bug Fixes
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* added forgotten yield in case of job preemption ([#148](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/148)) ([95e5fb7](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/95e5fb7cbeb6b874a83571328537b85493e10d97))
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## [0.10.1](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.10.0...v0.10.1) (2024-09-07)
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### Bug Fixes
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* logfile quoting and scancel error handling ([#140](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/140)) ([cb5d656](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/cb5d6568dfdfa3c2235bfe89a1e6ef294ab3ad8d))
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## [0.10.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.9.0...v0.10.0) (2024-08-23)
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### Features
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* in job stability ([#137](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/137)) ([c27f5f8](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/c27f5f8b4dcf7c2d9bc34fd4870d13ff24c0dfae))
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### Bug Fixes
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* add --parsable to sbatch call for a more robust output parsing ([#125](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/125)) ([5e41d05](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/5e41d0577593909f8f0f255c8de29141bfd0bbe3))
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* issue [#109](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/109) - preemption is no longer considered a failed status ([#132](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/132)) ([6dad273](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/6dad273b2f09ed8f10e3c26b92e2963c382e9fb8))
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## [0.9.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.8.0...v0.9.0) (2024-08-06)
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### Features
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* multicluster ([#56](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/56)) ([c0f8fee](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/c0f8feea745a4a97f44898a68effccb2b99834df))
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### Bug Fixes
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* fixed string for constraints - see issue [#58](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/58) ([#64](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/64)) ([89e10ff](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/89e10ff14d5705bb522efa74ed847e6a518da672))
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## [0.8.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.7.0...v0.8.0) (2024-07-12)
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### Features
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* cli ([#111](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/111)) ([b56837e](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/b56837efb61e3da89a2a5d0520e6d969ebf69137)), closes [#73](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/73)
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## [0.7.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.6.0...v0.7.0) (2024-06-25)
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### Features
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* warning if run in job ([#78](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/78)) ([257e830](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/257e830f28d7a226a0a7dad85703298677b9173c))
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### Bug Fixes
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* null byte account guess ([#81](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/81)) ([92d4445](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/92d44450bae805ef4b42387b9d27b295516d39da))
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### Documentation
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* added mini paragraph about Conda and Env Modules ([#42](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/42)) ([c821b5e](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/c821b5ea1b7a377421eee3964bf586bb82c47183))
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* added paragraphs about dynamic resource allocation ([#79](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/79)) ([06a1555](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/06a1555e0a1466576f2fea59a979d8d3e0c19df4))
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* storage update ([#80](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/80)) ([7e19560](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/7e19560731ca595687856ce45c8dd9e2fc5446cc))
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## [0.6.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.5.2...v0.6.0) (2024-06-07)
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### Features
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* will reject jobs, which attempt setting job names by 'slurm_extra' ([#93](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/93)) ([df2fd3d](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/df2fd3dfbbe1e0a606da719f33391d5c9fe9d679))
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## [0.5.2](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.5.1...v0.5.2) (2024-06-04)
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### Bug Fixes
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* [#97](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/97) preventing node confinment ([#98](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/98)) ([fa7877f](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/fa7877f8d086883ce74db75c3246b8c050720a62))
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## [0.5.1](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.5.0...v0.5.1) (2024-05-14)
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### Bug Fixes
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* allowing for accounts containing whitespace ([#86](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/86)) ([6993f2d](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/6993f2d7dd7c31fd34a79317df35ff80779f8a63))
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* proper line ending status message ([#87](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/87)) ([7b94aec](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/7b94aec8fdda5d2b0f8986154b6cb07d1954b7e8))
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## [0.5.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.4.5...v0.5.0) (2024-05-06)
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### Features
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* wildcards in comment string [#85](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/85) ([#88](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/88)) ([730cac0](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/730cac09c12a7038557ee937bc58c8c9e483c8f3))
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## [0.4.5](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.4.4...v0.4.5) (2024-04-17)
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### Bug Fixes
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* fix path typo ([#72](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/72)) ([f64fb5a](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/f64fb5adce9dc285c0b212af22d98b4289e8ce25))
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## [0.4.4](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.4.3...v0.4.4) (2024-04-15)
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### Miscellaneous Chores
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* release 0.4.4 ([6f2b966](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/6f2b96668b4e4f84cc1e8bcb5e123c97d3abdfd0))
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## [0.4.3](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.4.2...v0.4.3) (2024-04-12)
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### Bug Fixes
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* always create logdir before sbatch ([#67](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/67)) ([79fb961](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/79fb9612c1ddedd1eadc07741f17a940f2d989c6))
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## [0.4.2](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.4.1...v0.4.2) (2024-03-11)
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### Bug Fixes
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* adapt to latest snakemake-interface-executor-plugins ([#49](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/49)) ([8c7f5b1](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/8c7f5b1cbf085fb45a370c705c28a6fc030c9381))
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## [0.4.1](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.4.0...v0.4.1) (2024-02-29)
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### Bug Fixes
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* fixes issue [#40](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/40) - ntasks set explicitly ([#44](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/44)) ([f5c2c2c](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/f5c2c2c83b17442ab261619eadd9e6f71e39b772))
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## [0.4.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.3.2...v0.4.0) (2024-02-29)
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### Features
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* add wildcards to output and comment ([#35](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/35)) ([190500b](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/190500b1995cb34dd3cf8354ecfda36eae64ad2b))
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## [0.3.2](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.3.1...v0.3.2) (2024-02-24)
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### Bug Fixes
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* fix type error in job status checking if sacct fails ([6a197ae](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/6a197ae6d73061def6700af58b29f981dc323278))
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### Documentation
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* extended docs ([#37](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/37)) ([cf0407c](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/cf0407cc8115d3b64f486b2178b67118e16a12a7))
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## [0.3.1](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.3.0...v0.3.1) (2024-02-14)
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### Bug Fixes
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* Use sacct syntax that is compatible with slurm &lt; 20.11.0 ([#26](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/26)) ([c1591ff](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/c1591ff0d0eb7267cb5a64906f14e4aa47b9eac7))
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## [0.3.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.2.2...v0.3.0) (2024-02-01)
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### Features
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* print run id to log ([#10](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/10)) ([9ee8291](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/9ee82919ff42886bc5c64480c6fd1f74c4caf0d9))
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## [0.2.2](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.2.1...v0.2.2) (2024-02-01)
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### Bug Fixes
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* Typos in documentation ([#28](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/28)) ([326ce6c](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/326ce6ced3d946ebd485ce80bf03e8e07b1fc717))
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## [0.2.1](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.2.0...v0.2.1) (2024-01-16)
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### Bug Fixes
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* ensure proper handling of group jobs in combination with the slurm-jobstep executor ([f5c3d4c](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/f5c3d4c6b9bdcba68a512388d36d72d2700920bf))
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* remove limitation to single job in jobstep executor for group jobs ([18acfb6](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/18acfb6c4d1588c44941355d0f024c76de52bdbb))
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## [0.2.0](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.1.5...v0.2.0) (2024-01-10)
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### Features
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* include rule name as comment ([#16](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/16)) ([2e39b18](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/2e39b18688c8e80d4b78c23de01484374a7f065c))
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## [0.1.5](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.1.4...v0.1.5) (2024-01-05)
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### Bug Fixes
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* Force sacct to look at the last 2 days ([#9](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/9)) ([914265d](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/914265df76f1d6eab7ed0b38c61e123489ec0bc2))
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## [0.1.4](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.1.3...v0.1.4) (2023-12-08)
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### Documentation
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* metadata ([4edf9d5](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/4edf9d59f454333299b04f06855bc1522e481d56))
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## [0.1.3](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.1.2...v0.1.3) (2023-12-06)
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### Bug Fixes
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* Handle unresponsive sacct ([#5](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/5)) ([2f7ec1b](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/2f7ec1bb8cc809f0acba92c92819d57fd1affee1))
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### Documentation
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* update author encoding ([890bdb0](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/890bdb0d011bec922bdce6fa874f06a010ea8334))
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## [0.1.2](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.1.1...v0.1.2) (2023-11-20)
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### Bug Fixes
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* adapt to interface changes ([dcf9bc4](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/dcf9bc434a927a915eebfe9c3e99f13f74407ef5))
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## [0.1.1](https://github.com/snakemake/snakemake-executor-plugin-slurm/compare/v0.1.0...v0.1.1) (2023-10-29)
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### Bug Fixes
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* fix release process ([794bba8](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/794bba86df23ac4d1610f48434e631f0cc43b829))
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## 0.1.0 (2023-10-29)
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* adapt to API change ([4110331](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/411033198028eb8f894d1327300b5c10ce9618bb))
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* adapt to API changes ([75b2383](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/75b2383b914a3dab8e64a68213089b509f322691))
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* adapt to API changes in Snakemake 8 ([4c12093](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/4c1209399bfd0ce92fd698447be7fdbd3e526073))
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* adapt to changes in snakemake-interface-executor-plugins ([e73f71d](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/e73f71df9e0087afb58f2acd7e71b61b2740a263))
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* add dependency on slurm-jobstep ([fb5cdbc](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/fb5cdbc7694144dcb291846810b2b44261fc0a5d))
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* update to fixed version of snakemake-interface-executor-plugins ([#2](https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/2)) ([3dc72c6](https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/3dc72c69a5cbbfd150c21843adb16530c8fa7d34))
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‎README.md‎

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# Snakemake executor plugin: slurm
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# Snakemake executor plugin: pcluster-slurm
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[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/snakemake/snakemake-executor-plugin-slurm)
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For documentation, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html).
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For documentation, see the [Snakemake plugin catalog PLACEHOLDER for pcluster-slurm](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/pcluster-slurm.html).

‎docs/further.md‎

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## The general Idea
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To use this plugin, log in to your cluster's head node (sometimes called the "login" node), activate your environment as usual, and start Snakemake. Snakemake will then submit your jobs as cluster jobs.
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Upon creating a valid AWS Parallel Cluster (and one which uses slurm as the scheduler), to use this plugin: _a._ log in to your cluster's head node, _b._ activate your snakemake environment as usual (which should also have snakemake-executor-plugin-pcluster-slurm pip installed), and run a snakemake workflow with --executor pcluster-slurm. Snakemake will then submit your jobs as cluster jobs & `pcluster slurm` will manage creating compute nodes, bidding on them, managing budget constraints, spinning them down, etc. **It is magic really.**
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## Specifying Account and Partition
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## A Few Important `pcluster` `slurm` Peculiarities
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Most SLURM clusters have two mandatory resource indicators for
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accounting and scheduling, the account and a
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partition, respectively. These resources are usually
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omitted from Snakemake workflows in order to keep the workflow
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definition independent of the platform. However, it is also possible
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to specify them inside of the workflow as resources in the rule
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definition.
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- `slurm` for AWS Parallel Cluster does not ask for an account.
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- `--wrap` behaves oddly, and I just avoid its use and `<<EOF\n#!/bin/bash\n<submitstring>\nEOF` instead.
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- `--partition` is needed, you may set it with slurm_partition=`<your SLURM partition>` or `<your SLURM partition1>,<your SLURM partition2>,<your SLURM partition3>`.
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- `--comment` flag will be set to `RandD` unless a string is detected in the env variable `SMK_SLURM_COMMENT`. If project level tagging of resources is enabled in you pcluster cluster, this comment will need to match the per-user allowed projects specified in creating the ephemeral cluster. For more on project tagging, budget tracking and blocking on exceeded budgets, see HERE.
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## Inherited Docs, Not Verfied for `pcluster` `slurm`
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**W A R N I N G**
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_I do find it madeningly confusing as to how to set sbatch flags globally to apply to all rules... need to try again to figure this out._
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To specify them at the command line, define them as default resources:
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‎docs/intro.md‎

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[SLURM](https://slurm.schedmd.com/documentation.html) is a widely used
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batch system for performance compute clusters.
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This executor plugin allows to use it in a seamless and straightforward way.
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[AWS Parallel Cluster](https://aws.amazon.com/hpc/parallelcluster/) is a framework to deploy and manage dynamically scalable HPC clusters on AWS, running SLURM as the batch system, and `pcluster` manages all of the creating, configuring, and deleting of the cluster compute nodes. Nodes may be spot or dedicated. **note**, the `AWS Parallel Cluster` port of slurm has a few small, but critical differences from the standard slurm distribution. Importantly, `sacct` is not enabled, so any reliance on this command will break.
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This executor plugin allows to use slurm via AWS Parallel Cluster as an executor for snakemake via a `pcluster` headnode. For example usage of this executor, see: [daylily](https://github.com/DaylilyProject/daylily).

‎pyproject.toml‎

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[tool.poetry]
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name = "snakemake-executor-plugin-slurm"
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version = "0.11.0"
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description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
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name = "snakemake-executor-plugin-slurm-aws-parallel-cluster"
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version = "0.0.1"
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description = "A Snakemake executor plugin for submitting jobs to an AWS Parallel Cluster SLURM cluster."
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authors = [
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"Christian Meesters <meesters@uni-mainz.de>",
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"David Lähnemann <david.laehnemann@dkfz-heidelberg.de>",
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"Johannes Koester <johannes.koester@uni-due.de>",
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"John Major <john@daylilyinformatics.com>",
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"Cal <cal@daylilyinformatics.com>"
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]
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readme = "README.md"
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license = "MIT"
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repository = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
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documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html"
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keywords = ["snakemake", "plugin", "executor", "cluster", "slurm"]
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repository = "https://github.com/Daylily-Informatics/snakemake-executor-plugin-slurm-aws-parallel-cluster"
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documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/pcluster-slurm.NOTWRITTENYET.html"
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keywords = ["snakemake", "plugin", "executor", "cluster", "slurm", "pcluster", "aws", "parallel-compute", "parallel-cluster"]
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[tool.poetry.dependencies]
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python = "^3.11"

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