snakemake/snakemake issues and pull requests

#2389 - Conda environments executing Python scripts require Python versions compatible with the workflow's Snakemake version

Issue - State: closed - Opened by hypostulate over 1 year ago - 2 comments
Labels: bug

#2388 - chore(main): release 7.32.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 2 comments
Labels: autorelease: tagged

#2387 - docs: reference to "report" in tutorial, but no mention of that earlier

Issue - State: open - Opened by knarrff over 1 year ago
Labels: bug

#2386 - docs: fix a copy&paste (?) mistake

Pull Request - State: closed - Opened by knarrff over 1 year ago - 1 comment

#2385 - fix: print exceptions when job is not a shell job

Pull Request - State: closed - Opened by johanneskoester over 1 year ago - 1 comment

#2384 - Is there a way to run a snakemake rule only after another rule has finished without linking them by input/output?

Issue - State: closed - Opened by LukaLmelias over 1 year ago - 2 comments

#2383 - shadow: copy-minimal causes IsADirectoryError when input is directory

Issue - State: open - Opened by mobilegenome over 1 year ago - 2 comments
Labels: bug

#2382 - chore(main): release 7.31.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 2 comments
Labels: autorelease: tagged

#2381 - Kubernetes execution with GS remote fails to recognize remote "directory" and download it as a file

Issue - State: open - Opened by klin938 over 1 year ago
Labels: bug

#2380 - Apptainer not recognised

Issue - State: closed - Opened by RenscoHogers over 1 year ago - 6 comments
Labels: bug

#2379 - Shadowing not working as intended with absolute paths

Issue - State: open - Opened by gipert over 1 year ago - 1 comment
Labels: enhancement

#2378 - SLURM: Do not test empty account

Issue - State: closed - Opened by jindrahelcl over 1 year ago - 1 comment

#2377 - chore: use latest release of ansible roles for slurm setup

Pull Request - State: closed - Opened by johanneskoester over 1 year ago - 2 comments

#2376 - Wildcard constraints across modules

Issue - State: open - Opened by jsgounot over 1 year ago
Labels: bug

#2375 - style: add type linting

Pull Request - State: closed - Opened by Hocnonsense over 1 year ago - 4 comments

#2374 - 🐛 Nested config parsed as string when using --config

Issue - State: open - Opened by Wytamma over 1 year ago - 2 comments
Labels: bug

#2373 - Adding a param with a lambda that accesses `resources` to a rule that consumes a pipe causes a resource error in the subsequent rule when run with `--slurm`

Issue - State: open - Opened by hepcat72 over 1 year ago - 8 comments
Labels: bug

#2372 - fix: require python >=3.7 again (the python 3.9 dependency was unnecessary)

Pull Request - State: closed - Opened by dlaehnemann over 1 year ago - 7 comments

#2371 - chore(main): release 7.31.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#2370 - docs: update CHANGELOG.md: add minimum Python version bump

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 3 comments

#2369 - Add minimum Python version requirement bump to changelog

Issue - State: closed - Opened by corneliusroemer over 1 year ago - 1 comment

#2368 - docs: basics.rst: suggest VS Code instead of deprecated Atom as IDE

Pull Request - State: closed - Opened by dlaehnemann over 1 year ago - 1 comment

#2367 - chore(deps): Bump marocchino/sticky-pull-request-comment from 2.6.2 to 2.7.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#2366 - Error caused by inconsistent parsing of wildcards containing commas in Snakemake

Issue - State: open - Opened by ivazquez over 1 year ago - 2 comments
Labels: bug

#2364 - fix: updating of non-dict config values gives error

Pull Request - State: closed - Opened by padix-key over 1 year ago - 5 comments

#2363 - FTP.remote fails to download file.

Issue - State: closed - Opened by fgvieira over 1 year ago - 4 comments
Labels: bug

#2360 - Google Cloud Life Sciences Deprecation

Issue - State: closed - Opened by cademirch over 1 year ago - 20 comments
Labels: bug

#2357 - Job continuation. Keep output files

Issue - State: closed - Opened by ale94mleon over 1 year ago - 3 comments
Labels: enhancement

#2356 - fix: ensure lazy evaluation of resource functions/callables (this also entails, for now, a removal of the thread statistics in the yellow job stats table); further, added some clarifying sentences about resource function evaluation to the docs

Pull Request - State: closed - Opened by christopher-schroeder over 1 year ago - 1 comment

#2354 - Snakemake very slow on large workflow

Issue - State: closed - Opened by fgvieira over 1 year ago - 2 comments
Labels: bug

#2350 - Snakefile is run a second time if rule contains `run` directive

Issue - State: open - Opened by padix-key over 1 year ago - 2 comments
Labels: bug

#2347 - fix: wms-monitor now gets data in correct json format

Pull Request - State: closed - Opened by bilgehannevruz over 1 year ago - 1 comment

#2344 - feat: implement semantic helper functions for input and param function handling

Pull Request - State: closed - Opened by johanneskoester over 1 year ago - 3 comments

#2343 - Snakemake should not require mamba

Issue - State: closed - Opened by BEFH over 1 year ago - 1 comment
Labels: bug

#2342 - chore: Remove references to allows_directories

Pull Request - State: closed - Opened by s-mustafa over 1 year ago - 1 comment

#2341 - refactor: define consistent abstract base classes for jobs

Pull Request - State: closed - Opened by johanneskoester over 1 year ago - 3 comments

#2340 - fix: Enable values with an = sign in default_resources

Pull Request - State: closed - Opened by ohlmann over 1 year ago - 3 comments

#2339 - Workflow not being executed in parallel on batch computing nodes (SLURM cluster grouped execution)

Issue - State: open - Opened by gipert over 1 year ago - 4 comments

#2338 - chore(main): release 7.30.2

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 2 comments
Labels: autorelease: tagged

#2334 - singularity version issue

Issue - State: closed - Opened by epersoon over 1 year ago - 2 comments
Labels: bug

#2331 - workflow.source_path does not work as expected

Issue - State: open - Opened by chrarnold over 1 year ago - 5 comments
Labels: bug

#2327 - too many resources with grouped jobs

Issue - State: open - Opened by christopher-schroeder over 1 year ago - 2 comments
Labels: bug

#2324 - feat: add native support for execution on AWS Batch

Pull Request - State: open - Opened by wleepang over 1 year ago - 9 comments

#2322 - Add "micromamba" as an option for --conda-frontend

Issue - State: open - Opened by magmir71 over 1 year ago - 6 comments
Labels: enhancement

#2320 - Slurm account names with spaces in result in "The given account {account} appears to be invalid"

Issue - State: open - Opened by benjeffery over 1 year ago - 5 comments
Labels: bug

#2318 - feat: Add support for Google Service Accounts and GCE VM network configuration

Pull Request - State: closed - Opened by johntbates over 1 year ago - 2 comments

#2317 - Slurm resource allocation and usage

Issue - State: closed - Opened by ftabaro over 1 year ago - 3 comments
Labels: enhancement

#2305 - feat: support for external executor plugins

Pull Request - State: closed - Opened by vsoch over 1 year ago - 24 comments

#2304 - snakemake python 3.12 support

Issue - State: closed - Opened by maarten-k over 1 year ago - 3 comments
Labels: bug

#2291 - fix: Update init.py to move "file" param to "print"

Pull Request - State: closed - Opened by Hocnonsense over 1 year ago - 1 comment

#2290 - Specification of default_resources in a profile cannot contain = signs

Issue - State: closed - Opened by ohlmann over 1 year ago - 1 comment
Labels: bug

#2289 - feat: Use of conda directive for shell function calls from 'run' scripts.

Pull Request - State: open - Opened by mhulsman over 1 year ago - 6 comments

#2288 - Error trying to use conda env by name if Snakemake is not installed in base

Issue - State: closed - Opened by tdido over 1 year ago - 2 comments
Labels: bug

#2282 - `--max_jobs_per_second` is ignored.

Issue - State: open - Opened by xapple over 1 year ago - 5 comments
Labels: bug

#2281 - Type check for `cpus_per_task` does not work

Issue - State: closed - Opened by FFroehlich over 1 year ago - 2 comments
Labels: bug

#2280 - slurm hang in SLURM mode

Issue - State: closed - Opened by Zepeng-Mu over 1 year ago - 1 comment
Labels: bug

#2279 - Add "walltime" as an alias for the "runtime" resource

Issue - State: closed - Opened by tdido over 1 year ago - 2 comments
Labels: enhancement

#2276 - :bug: Snakemake-minimal error reading config file

Issue - State: open - Opened by enryH over 1 year ago - 5 comments
Labels: bug

#2274 - Snakemake crashes with a KeyError when using `--immediate-submit`

Issue - State: open - Opened by xapple over 1 year ago - 2 comments

#2272 - feat!: #2271 Replace list-version-changes with list-conda-env-changes

Pull Request - State: open - Opened by nigiord almost 2 years ago - 3 comments

#2271 - --list-version-changes should become --list-software-env-changes

Issue - State: open - Opened by nigiord almost 2 years ago - 1 comment
Labels: enhancement

#2270 - chore(main): release 7.26.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 2 comments
Labels: autorelease: tagged

#2269 - feat: allow config files to be processed with YTE

Pull Request - State: closed - Opened by johanneskoester almost 2 years ago - 2 comments

#2268 - fix: add missing spaces between lines that get concatenated.

Pull Request - State: closed - Opened by echoix almost 2 years ago - 2 comments

#2267 - Add mem_mib to documentation

Issue - State: open - Opened by danpal96 almost 2 years ago - 1 comment
Labels: enhancement

#2266 - fix: remote GS builds too many inventories; io:collect_mtime always uses uncached mtime

Pull Request - State: open - Opened by cademirch almost 2 years ago - 7 comments

#2265 - refactor: removed unused import

Pull Request - State: open - Opened by maarten-k almost 2 years ago - 1 comment

#2264 - feat: add the --ancient command line option.

Pull Request - State: open - Opened by nh13 almost 2 years ago - 4 comments

#2263 - feat: Allow the environment variable SNAKEMAKE_CONDA_PREFIX to be present without --use-conda

Pull Request - State: open - Opened by mrvollger almost 2 years ago - 2 comments

#2262 - Offline option for using wrappers

Issue - State: open - Opened by hazmup almost 2 years ago
Labels: enhancement

#2261 - snakemake long benchmark name results in "Removing output files of failed job generate since they might be corrupted:"

Issue - State: open - Opened by KalinNonchev almost 2 years ago - 3 comments
Labels: bug

GitHub / snakemake/snakemake issues and pull requests