snakemake/snakemake-executor-plugin-slurm

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A Snakemake executor plugin for submitting jobs to a SLURM cluster

Stars: 55
Forks: 57
Open beginner issues: 0
Indexed issues: 39
Avg merge: 40m
Merged PRs (30d): 1

Dominant language: Python
License: MIT
Last GitHub push: Sep 17, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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39 open issues indexed

Allow use of SLURM defaults instead of plugin defaults Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

snakemake/snakemake-executor-plugin-slurm#475 · 4 comments · Opened Jul 7, 2026
Use workflow ID as slurm UUID Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

snakemake/snakemake-executor-plugin-slurm#474 · 1 comment · Opened Jul 3, 2026
Array-job mode leaks scheduler -j slots and deadlocks ("Selected jobs: 0" with many ready jobs) Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

snakemake/snakemake-executor-plugin-slurm#473 · 3 comments · Opened Jul 3, 2026
Unexpected interaction between local() inputs, Slurm execution, and fs staging in Snakemake Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

snakemake/snakemake-executor-plugin-slurm#471 · Opened Jun 17, 2026
Group jobs run sequentially on Slurm Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

snakemake/snakemake-executor-plugin-slurm#469 · 2 comments · Opened Jun 9, 2026
Economize slurm RPC calls, omit srun from jobstep plugin? Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

snakemake/snakemake-executor-plugin-slurm#467 · 1 comment · Opened Jun 5, 2026
Multiple --gres arguments not supported Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

snakemake/snakemake-executor-plugin-slurm#466 · 1 comment · Opened Jun 1, 2026
Dry-run crashes with KeyError when a checkpoint-driven grouped job is present Open

Difficulty 4/5 3-5 days Newbie friendliness 50/100

snakemake/snakemake-executor-plugin-slurm#463 · 3 comments · Opened May 25, 2026
Installing via bioconda installs incompatible version of slurm-jobstep executor Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

snakemake/snakemake-executor-plugin-slurm#461 · 5 comments · Opened May 20, 2026
Unexpexted behavior with multiple GPUs Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

snakemake/snakemake-executor-plugin-slurm#459 · 7 comments · Opened May 11, 2026
Support batching many short jobs into a single serial SLURM submission without inflating resource requests Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

snakemake/snakemake-executor-plugin-slurm#458 · 2 comments · Opened May 7, 2026
Add --slurm_extra_args Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

snakemake/snakemake-executor-plugin-slurm#457 · 4 comments · Opened May 6, 2026
Silent failure when grouped job runtime exceeds partition time limit Open

Difficulty 3/5 1-2 days Newbie friendliness 57/100

snakemake/snakemake-executor-plugin-slurm#456 · 1 comment · Opened Apr 28, 2026
return all best partitions in case of tie Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

snakemake/snakemake-executor-plugin-slurm#455 · Opened Apr 22, 2026
How to see differences in html files that are part of the plugin catalog Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

snakemake/snakemake-executor-plugin-slurm#449 · 1 comment · Opened Apr 2, 2026
Job arrays across different wildcards may not create output directories Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

snakemake/snakemake-executor-plugin-slurm#447 · 2 comments · Opened Mar 30, 2026
docs: link to Snakemake main for group job resources Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

snakemake/snakemake-executor-plugin-slurm#443 · Opened Mar 18, 2026
slurm_account error when the account is a builtin python function Open

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

snakemake/snakemake-executor-plugin-slurm#354 · 11 comments · 1 reaction · Opened Sep 11, 2025
no-requeue Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

snakemake/snakemake-executor-plugin-slurm#353 · 5 comments · Opened Sep 10, 2025
OOM handling for jobstep plugin Open

bug/fix

snakemake/snakemake-executor-plugin-slurm#348 · 18 comments · 1 assignee · Opened Aug 26, 2025
Default mem_mb_per_cpu takes precedence over Snakefile mem_mb Open

stale

Difficulty 4/5 3-5 days Newbie friendliness 45/100

snakemake/snakemake-executor-plugin-slurm#335 · 2 comments · Opened Jul 30, 2025
`resolve_ctls_from_dns_srv` if running within interactive/compute node. Open

stale

Difficulty 4/5 3-5 days Newbie friendliness 35/100

snakemake/snakemake-executor-plugin-slurm#334 · 2 comments · Opened Jul 28, 2025
failed to open persistent connection to host:slurm:6819: Connection refused Open

stale

snakemake/snakemake-executor-plugin-slurm#331 · 7 comments · 1 assignee · Opened Jul 9, 2025
clarify implementation of `--seconds-between-status-checks` and `--max-status-checks-per-secon` Open

stale

Difficulty 4/5 3-5 days Newbie friendliness 30/100

snakemake/snakemake-executor-plugin-slurm#319 · 1 comment · 1 reaction · Opened Jun 2, 2025
SBATCH --mem-per-cpu in call is mem_mb_per_cpu x threads Open

bug/fix stale

Difficulty 3/5 1-2 days Newbie friendliness 42/100

snakemake/snakemake-executor-plugin-slurm#317 · 2 comments · Opened Jun 2, 2025
catch errors from `delete_empty_dirs` Open

bug/fix stale

snakemake/snakemake-executor-plugin-slurm#315 · 1 comment · 1 assignee · Opened May 26, 2025
SLURM --retries now run inside individual SLURM submissions in addition to re-submissions Open

stale

Difficulty 4/5 3-5 days Newbie friendliness 50/100

snakemake/snakemake-executor-plugin-slurm#284 · 15 comments · Opened May 14, 2025
Default to use `--container` param in job submission Open

stale

Difficulty 3/5 1-2 days Newbie friendliness 38/100

snakemake/snakemake-executor-plugin-slurm#257 · 6 comments · Opened Apr 27, 2025
Jobs submitted multiple times in different groups Open

stale

Difficulty 4/5 3-5 days Newbie friendliness 35/100

snakemake/snakemake-executor-plugin-slurm#253 · 5 comments · Opened Apr 10, 2025
Localrules hang after completion Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

snakemake/snakemake-executor-plugin-slurm#252 · 7 comments · Opened Apr 2, 2025
Allow signalling applications upon job cancellation Open

enhancement stale

snakemake/snakemake-executor-plugin-slurm#243 · 4 comments · 1 assignee · Opened Mar 18, 2025
Signal Forwarding to Jobscripts Open

enhancement

snakemake/snakemake-executor-plugin-slurm#242 · 6 comments · 1 assignee · Opened Mar 18, 2025
Best way to bundle ALL jobs together into a single Slurm allocation? Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

snakemake/snakemake-executor-plugin-slurm#181 · 7 comments · Opened Jan 14, 2025
Allow simultaneous use of envmodules and conda environment Open

stale

Difficulty 4/5 3-5 days Newbie friendliness 38/100

snakemake/snakemake-executor-plugin-slurm#156 · 5 comments · Opened Oct 14, 2024
Can't unquote in slurm_extra Open

stale

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

snakemake/snakemake-executor-plugin-slurm#120 · 3 comments · 4 reactions · Opened Jul 31, 2024
Determine dynamic resources depending on retry reason? Open

discussion stale

Difficulty 5/5 Over a week Newbie friendliness 25/100

snakemake/snakemake-executor-plugin-slurm#65 · 7 comments · 2 reactions · Opened Apr 11, 2024
Dynamic runtime resource fails with SLURM Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

snakemake/snakemake-executor-plugin-slurm#62 · 5 comments · Opened Apr 5, 2024
Dynamic determination of queue Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

snakemake/snakemake-executor-plugin-slurm#61 · 5 comments · Opened Apr 4, 2024
Differences in SLURM command between what Snakemake says it runs and what is actually run Open

stale

snakemake/snakemake-executor-plugin-slurm#57 · 9 comments · 1 assignee · Opened Apr 2, 2024

snakemake/snakemake-executor-plugin-slurm

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