snakemake/snakemake issues and pull requests

#3188 - fix: correctly set params in bash scripts

Pull Request - State: closed - Opened by mbhall88 4 months ago - 4 comments

#3187 - Params unbound in Bash scripts

Issue - State: closed - Opened by mbhall88 4 months ago
Labels: bug

#3187 - Params unbound in Bash scripts

Issue - State: closed - Opened by mbhall88 4 months ago
Labels: bug

#3186 - Global container image specification overridden by module import

Issue - State: open - Opened by laf070810 4 months ago
Labels: bug

#3186 - Global container image specification overridden by module import

Issue - State: open - Opened by laf070810 4 months ago
Labels: bug

#3185 - chore(main): release 8.25.2

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 3 comments
Labels: autorelease: tagged

#3185 - chore(main): release 8.25.2

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 3 comments
Labels: autorelease: tagged

#3184 - fix: include conda pinnings, conda post deploy script, and env modules for detection of software stack changes and corresponding rerun triggers

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3183 - rust-script >= 0.23.0 fails with current version of snakemake

Issue - State: closed - Opened by jackerschott 4 months ago - 3 comments
Labels: bug

#3182 - chore: do not compare checksum after tailwind download, as the returned CSS is not stable for even the same release

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 3 comments

#3182 - chore: do not compare checksum after tailwind download, as the returned CSS is not stable for even the same release

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 3 comments

#3181 - fix: ensure correct topological order when touching group job outputs

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 3 comments

#3181 - fix: ensure correct topological order when touching group job outputs

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 3 comments

#3180 - chore(main): release 8.25.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 3 comments
Labels: autorelease: tagged

#3180 - chore(main): release 8.25.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 3 comments
Labels: autorelease: tagged

#3179 - Running Snakemake with slurm executor returns AttributeError

Issue - State: closed - Opened by ericxytong 4 months ago - 1 comment

#3179 - Running Snakemake with slurm executor returns AttributeError

Issue - State: closed - Opened by ericxytong 4 months ago - 1 comment

#3178 - Add more details to log lines like "Finished job 7."

Issue - State: open - Opened by corneliusroemer 4 months ago - 1 comment
Labels: enhancement

#3178 - Add more details to log lines like "Finished job 7."

Issue - State: open - Opened by corneliusroemer 4 months ago - 1 comment
Labels: enhancement

#3177 - Helper function for turning Python filenames into module names (or vice versa)

Issue - State: open - Opened by edbennett 4 months ago
Labels: enhancement

#3177 - Helper function for turning Python filenames into module names (or vice versa)

Issue - State: open - Opened by edbennett 4 months ago
Labels: enhancement

#3176 - refactor: Remove datrie dependency

Pull Request - State: open - Opened by leoschwarz 4 months ago - 14 comments

#3176 - refactor: Remove datrie dependency

Pull Request - State: open - Opened by leoschwarz 4 months ago - 14 comments

#3175 - fix: ensure version agnostic robust pickling of pandas, polars and numpy data structures passed as params to Python scripts or notebooks

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3175 - fix: ensure version agnostic robust pickling of pandas, polars and numpy data structures passed as params to Python scripts or notebooks

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3174 - fix: skip storage object when cloning flags for shadowed IO

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3174 - fix: skip storage object when cloning flags for shadowed IO

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3171 - feat: allow to mark input files of rules as ancient via the API or command line interface (and thereby also via workflow specific profiles). Putting this into a workflow specific profile (or specifying as argument) allows to overrule rerun triggers caused by file modification dates where the user knows better.

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 3 comments

#3171 - feat: allow to mark input files of rules as ancient via the API or command line interface (and thereby also via workflow specific profiles). Putting this into a workflow specific profile (or specifying as argument) allows to overrule rerun triggers caused by file modification dates where the user knows better.

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 3 comments

#3170 - chore(main): release 8.25.0

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 3 comments
Labels: autorelease: tagged

#3165 - clock skew error with grouped rules

Issue - State: open - Opened by mbhall88 4 months ago - 11 comments

#3164 - fix: Cannot change working directory when R script hosted on GitHub with source

Pull Request - State: open - Opened by rschauner 4 months ago - 2 comments

#3163 - More specific recommendations in Raise CreateCondaEnvironmentException: Conda must be version 24.7.1 or later,

Issue - State: open - Opened by tito-abbo 4 months ago - 5 comments
Labels: enhancement

#3163 - More specific recommendations in Raise CreateCondaEnvironmentException: Conda must be version 24.7.1 or later,

Issue - State: open - Opened by tito-abbo 4 months ago - 5 comments
Labels: enhancement

#3156 - docs: use "dictionary" not "array" wording in config docs

Pull Request - State: closed - Opened by ressy 4 months ago - 5 comments

#3156 - docs: use "dictionary" not "array" wording in config docs

Pull Request - State: closed - Opened by ressy 4 months ago - 5 comments

#3155 - fix: Pass `host` attribute to `GitlabFile` instantiation within class methods

Pull Request - State: closed - Opened by phmoferring 4 months ago - 2 comments

#3155 - fix: Pass `host` attribute to `GitlabFile` instantiation within class methods

Pull Request - State: closed - Opened by phmoferring 4 months ago - 2 comments

#3151 - Callbacks from DAG .execute_workflow() needed for progress bar

Issue - State: open - Opened by peterjc 4 months ago - 12 comments
Labels: enhancement

#3151 - Callbacks from DAG .execute_workflow() needed for progress bar

Issue - State: open - Opened by peterjc 4 months ago - 4 comments
Labels: enhancement

#3148 - fix: mtime of script or notebook not triggering workflow without metadata

Pull Request - State: open - Opened by laf070810 4 months ago - 2 comments

#3148 - fix: mtime of script or notebook not triggering workflow without metadata

Pull Request - State: open - Opened by laf070810 4 months ago - 2 comments

#3140 - feat: more robust parameter and code change detection and transparent reporting of detected changes

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 4 comments

#3140 - feat: more robust parameter and code change detection and transparent reporting of detected changes

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 4 comments

#3138 - chore(deps): allow pulp 2.9

Pull Request - State: open - Opened by musicinmybrain 4 months ago - 2 comments

#3137 - `--generate-unit-tests` will raise error in `8.20.1` or newer version

Issue - State: open - Opened by jiangyun-fun 4 months ago - 2 comments
Labels: bug

#3136 - Question: Can you make an execute a snakemake workflow in pure python?

Issue - State: open - Opened by harrymatthews50 4 months ago

#3135 - fix: configfile `group` and `group-components` were not being registered

Pull Request - State: open - Opened by jjjermiah 4 months ago - 2 comments

#3134 - chore(main): release 8.21.0

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 2 comments
Labels: autorelease: tagged

#3133 - chore: configure CI to allow apptainer to run properly again

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3132 - feat: support for specifying conda envs as directories

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3131 - fix: notebook execution for apptainer

Pull Request - State: closed - Opened by laf070810 4 months ago - 5 comments

#3130 - `run` directive will reinitialize the global variables

Issue - State: open - Opened by jiangyun-fun 4 months ago
Labels: bug

#3129 - fix: better error handling in evaluate function

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3128 - Running Snakemake --touch gives PulpSolverError

Issue - State: open - Opened by tbenavi1 4 months ago - 4 comments
Labels: bug

#3127 - fix: install conda in container image

Pull Request - State: closed - Opened by johanneskoester 4 months ago - 2 comments

#3126 - fix: profile parsing groups and group-components

Pull Request - State: closed - Opened by jjjermiah 4 months ago - 2 comments

#3125 - chore(main): release 8.20.7

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 3 comments
Labels: autorelease: tagged

#3124 - Support standard Python virtual env. for rules

Issue - State: open - Opened by ccoulombe 5 months ago - 5 comments
Labels: enhancement

#3123 - Announcement: Snakemake hackathon 2025 at CERN, call for participants!

Issue - State: open - Opened by johanneskoester 5 months ago
Labels: enhancement

#3122 - chore(main): release 8.20.6

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 3 comments
Labels: autorelease: tagged

#3121 - fix: rely on conda >24.7.1 for conda env deployment and deprecate mamba support

Pull Request - State: closed - Opened by johanneskoester 5 months ago - 2 comments

#3120 - Remove temporary paramiko version constraint

Issue - State: open - Opened by coderabbitai[bot] 5 months ago
Labels: enhancement

#3119 - Remove temporary paramiko version constraint

Issue - State: open - Opened by coderabbitai[bot] 5 months ago
Labels: enhancement

#3118 - snakemake --dag fails if there are ambiguities because workflow.execution_settings is None

Issue - State: open - Opened by tesujimath 5 months ago - 1 comment
Labels: bug

#3117 - fix: adapt to changes in mamba 2.0

Pull Request - State: closed - Opened by johanneskoester 5 months ago - 4 comments

#3116 - fix: remote pre-command not installing all required storage plugins

Pull Request - State: closed - Opened by jjjermiah 5 months ago - 3 comments

#3115 - feat: Initial attempt at adding a --any-of feature

Pull Request - State: open - Opened by WeatherGod 5 months ago - 5 comments

#3114 - refactor: simplify plugin registry calling

Pull Request - State: open - Opened by johanneskoester 5 months ago - 2 comments

#3113 - feat: add two new schedulers

Pull Request - State: open - Opened by fgvieira 5 months ago - 6 comments

#3112 - feat: subsample jobs to speed-up scheduler

Pull Request - State: open - Opened by fgvieira 5 months ago - 2 comments

#3111 - fix: snakemake deployment update for mamba > 2.0.0

Pull Request - State: closed - Opened by aabiddanda 5 months ago - 7 comments

#3110 - fix: remove paramiko dependency as issue has been fixed

Pull Request - State: open - Opened by fgvieira 5 months ago - 2 comments

#3109 - feat: switch from toposort to graphlib

Pull Request - State: open - Opened by fgvieira 5 months ago - 3 comments

#3108 - mamba 2.0.0 doesn't support the `--no-default-packages` option

Issue - State: open - Opened by edbennett 5 months ago - 2 comments
Labels: bug

#3107 - feat: WIP Logging refactor

Pull Request - State: open - Opened by cademirch 5 months ago - 22 comments

#3106 - Be able to depend on individual dataset(s) within an HDF5 file

Issue - State: open - Opened by edbennett 5 months ago
Labels: enhancement

#3105 - snakemake dependency 'datrie' requires fragile C extention compiles on modern python

Issue - State: open - Opened by samimia-swks 5 months ago - 1 comment
Labels: bug

#3104 - feat: Add commentstring for vim plugin

Pull Request - State: closed - Opened by vandalt 5 months ago - 2 comments

#3103 - fix: fixed check for remote conda env pinning and post-deploy files; fixed conda env cleanup

Pull Request - State: closed - Opened by johanneskoester 5 months ago - 2 comments

#3102 - Enhance Report Plugin Flexibility: Template Language Support, File Rendering Options, and Report Structure Customization

Issue - State: open - Opened by MatthiasLienhard 5 months ago
Labels: enhancement

#3093 - fix: cache conda envs to fix performance regression introduced in https://github.com/snakemake/snakemake/pull/1300

Pull Request - State: closed - Opened by johanneskoester 5 months ago - 2 comments

GitHub / snakemake/snakemake issues and pull requests