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snakemake

14 indexed repositories · View on GitHub

snakemake
This is the development home of the workflow management system Snakemake. For general information, see

Python · 2877 stars
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see

Python · 255 stars
snakefmt
The uncompromising Snakemake code formatter

Python · 196 stars
snakemake-executor-plugin-slurm
A Snakemake executor plugin for submitting jobs to a SLURM cluster

Python · 55 stars
snakemake-workflow-catalog
A statically generated catalog of available Snakemake workflows

Python · 37 stars
snakemake-executor-plugin-aws-batch
A Snakemake executor plugin for AWS Batch

Python · 12 stars
snakemake-report-plugin-rocrate
Snakemake Report Plugin to automatically create Workflow Run RO-Crate after workflow runs holding all metadata of that workflow

Python · 2 stars
snakemake-software-deployment-plugin-conda
A Snakemake software deployment plugin for using conda packages. Implemented using py-rattler.

Python · 2 stars
snakemake-infrastructure-profiles
The snakemake-profiles repository is an effort to create configuration profiles for executing Snakemake in specific institutional cluster...

Shell · 1 star
snakemake-executor-plugin-slurm-jobstep
A Snakemake executor plugin for running srun jobs inside of SLURM jobs (meant for internal use by snakemake-executor-plugin-slurm)

Python · 1 star
snakemake-software-deployment-plugin-envmodules
Snakemake software deployment plugin for environment modules

Python · 0 stars
snakemake-interface-common
Common functions and classes for Snakemake and its plugins

Python · 0 stars
snakemake-hpc-teaching-material

TeX · 0 stars
snakemake-interface-software-deployment-plugins
A stable interface for Snakemake software deployment plugins

Python · 0 stars

Beginner friendly Everything

Open All

Outdated description of conda environment naming Open

bug documentation good first issue

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

snakemake/snakemake#4319 · 4 comments · Opened Sep 18, 2026
Minio not available on dockerhub, switch to silo Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

snakemake/snakemake#4316 · Opened Sep 17, 2026
Roadmap: editor in Frankfurt Open

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

snakemake/snakemake-hpc-teaching-material#38 · Opened Sep 16, 2026
`unpack`ing a checkpoint gives `AttributeError: 'InputFiles' object has no attribute ...` in params function Open

bug

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

snakemake/snakemake#4312 · Opened Sep 9, 2026
0.6.1: dropping `SLURM_CONF` from the nested `srun` environment breaks every job step on clusters with a non-default config path Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

snakemake/snakemake-executor-plugin-slurm-jobstep#54 · 1 comment · Opened Sep 6, 2026
Request: relax sqlmodel dependency upper bound Open

Difficulty 1/5 Under an hour Newbie friendliness 88/100

snakemake/snakemake#4308 · 1 comment · Opened Sep 5, 2026
Publishing snakemake-software-deployment plugin for EESSI Open

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

snakemake/snakemake#4304 · Opened Sep 2, 2026
config KeyError for unused rules Open

enhancement

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

snakemake/snakemake#4303 · Opened Sep 1, 2026
`--target-jobs` removes literal quotes from wildcard value boundaries Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 65/100

snakemake/snakemake#4298 · Opened Aug 28, 2026
Estimate energy consumption and CO2 emissions of workflow runs Open

enhancement

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

snakemake/snakemake#4295 · 1 reaction · Opened Aug 26, 2026
Include parameter values in dry run output. Open

enhancement

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

snakemake/snakemake#4290 · Opened Aug 24, 2026
Usage of old wrapers leading to TypeError for snakemake > 9.17.3 Open

bug

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

snakemake/snakemake#4287 · 1 comment · Opened Aug 22, 2026
RuntimeWarning: coroutine 'InputFiles._predicated_size_files.<locals>.sizes' was never awaited Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

snakemake/snakemake#4280 · Opened Aug 17, 2026
Raise an error, if a --workflow-profile directory does not exist Open

enhancement

snakemake/snakemake#4276 · 1 assignee · Opened Aug 13, 2026
workdir keyword is not properly working Open

bug

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

snakemake/snakemake#4271 · Opened Aug 7, 2026
0.6.1: dropping `SLURM_MEM_PER_CPU` from the nested `srun` environment makes steps fall back to `DefMemPerCPU` and get OOM-killed Open

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

snakemake/snakemake-executor-plugin-slurm-jobstep#53 · 2 comments · Opened Aug 5, 2026
force() flag as opposite to ancient() Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 38/100

snakemake/snakemake#4254 · Opened Jul 23, 2026
Fix Incorrect Workflow, Tool, and Parameter Modeling in Generated RO-Crates Open

snakemake/snakemake-report-plugin-rocrate#7 · 7 comments · 1 assignee · Opened Jul 17, 2026
Logging error with groups - KeyError: 'name' Open

bug

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

snakemake/snakemake#4248 · 3 comments · Opened Jul 16, 2026
PermissionError during provenance generation when an external file acts as both input and output on read-only filesystems Open

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

snakemake/snakemake-report-plugin-rocrate#5 · Opened Jul 16, 2026
`bio/salmon/index` (and `bio/salmon/quant`) example declares `index.tct`/`index.tdct` as unconditional outputs, but Salmon only creates them for small references Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 70/100

snakemake/snakemake-wrappers#5543 · 2 comments · Opened Jul 15, 2026
kernel directive to specify notebook kernel Open

enhancement

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

snakemake/snakemake#4243 · Opened Jul 10, 2026
Allow notebook directive to save copy as output Open

enhancement

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

snakemake/snakemake#4242 · Opened Jul 10, 2026
Slow job scheduling on high-latency filesystems Open

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

snakemake/snakemake#4240 · 5 comments · Opened Jul 9, 2026
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
Overwriting a rule from a module messes up the workflow Open

bug

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

snakemake/snakemake#4238 · 1 comment · Opened Jul 3, 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
Ideas for future database set-up Open

enhancement help wanted question

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

snakemake/snakemake-workflow-catalog#86 · 3 comments · Opened Jun 24, 2026
Notebooks paths are made absolute and cannot be linked to upstream rules anymore Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 52/100

snakemake/snakemake#4236 · 1 comment · Opened Jun 22, 2026
`--print-compilation` ignores SyntaxErrors Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

snakemake/snakemake#4235 · 1 comment · Opened Jun 19, 2026
Unexpected interaction between local() inputs, Slurm execution, and FS staging Open

bug

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

snakemake/snakemake#4233 · Opened Jun 18, 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
Unable to obtain modification time of a dropped file (datalad/git-annex) Open

bug

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

snakemake/snakemake#4229 · 1 comment · Opened Jun 13, 2026
how to launch containerized snakemake that submits jobscripts using the same container Open

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

snakemake/snakemake#4226 · Opened Jun 10, 2026
fix for benchmark when rule using run clause reports no stats Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

snakemake/snakemake#4224 · Opened Jun 10, 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
perf: snakemake dry-run spends most wall-clock on conda verification and eager module imports Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

snakemake/snakemake#4220 · 1 comment · Opened Jun 6, 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
Remote scripts do not trigger job re-execution when updated Open

bug

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

snakemake/snakemake#4217 · Opened Jun 4, 2026
Race condition in output_mintime with temp inputs may give an error Open

bug

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

snakemake/snakemake#4213 · Opened Jun 2, 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 35/100

snakemake/snakemake#4202 · 1 comment · Opened May 25, 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
Creating a private copy of the snakemake workflow catalog Open

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

snakemake/snakemake-workflow-catalog#79 · 2 comments · Opened May 24, 2026
Question about modular design Open

bug

snakemake/snakemake#4201 · 2 comments · 1 assignee · Opened May 23, 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
Skills for claude code Open

enhancement

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

snakemake/snakemake#4198 · 10 comments · 1 reaction · Opened May 20, 2026
Wildcard constraints applied before pathvar expansion Open

bug

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

snakemake/snakemake#4197 · Opened May 20, 2026
Add support for marimo notebooks Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

snakemake/snakemake#4195 · 1 comment · 2 reactions · Opened May 19, 2026

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