snakemake/snakemake

Issues

• Using snakemake -q all hides SLURM error messages

  #3173 opened 2 months ago by peterjc
  4

• Using snakemake -q all does not silence stdout and stderr from rules

  #3152 opened 2 months ago by peterjc
  5

• Snakemake not finding input files

  #3210 opened a month ago by Dm572
  1

• clock skew error with grouped rules

  #3165 opened 21 days ago by mbhall88
  16

• Wildcard values modified in some circumstances

  #3221 opened a month ago by irr-github
  0

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

  #3108 opened 3 months ago by edbennett
  4

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

  #3183 opened a month ago by jackerschott
  3

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

  #3137 opened 2 months ago by jiangyun-fun
  2

• Better way to signal an error to the user

  #3214 opened a month ago by jlumpe
  1

• Add more details to log lines like "Finished job 7."

  #3178 opened 2 months ago by corneliusroemer
  1

• Code changes in python rules no longer trigger re-running of workflows

  #3213 opened a month ago by royjacobson
  0

• `FileNotFoundError` for `global.yaml` When Loading Module via `github()`

  #3212 opened a month ago by sreichl
  0

• Snakemake Fails with Space in Path When Using run Statement

  #3211 opened a month ago by Wytamma
  0

• Add key to rule definitions to postpone scheduling of a job based on runtime-dependent user criteria

  #3209 opened a month ago by wiedenhoeft
  0

• Modernize logging and support for monitoring as plugins

  #3207 opened a month ago by JRodez
  1

• Options for batch runs

  #3206 opened a month ago by wiedenhoeft
  0

• Snakemake resources does not trigger GPU node-pool on kubernetes.

  #3205 opened a month ago by mrburke00
  0

• conda info --json returned non-zero exit status 127

  #3202 opened a month ago by farchaab
  0

• locally detected cores determine remote max thread level

  #3191 opened 2 months ago by cmeesters
  2

• Params unbound in Bash scripts

  #3187 opened a month ago by mbhall88
  0

• Support for wrappers in private repositories

  #3194 opened a month ago by mhorlacher
  0

• wildcard_constraints bad character range

  #3190 opened a month ago by susheelbhanu
  3

• snakemake --cleanup-metadata appears broken in 8.24.0 and 8.25.2

  #3193 opened 2 months ago by daknuett
  0

• AttributeError when using existing conda environment with checkpoint

  #3192 opened 2 months ago by johnne
  0

• Global container image specification overridden by module import

  #3186 opened 2 months ago by laf070810
  0

• More specific recommendations in Raise CreateCondaEnvironmentException: Conda must be version 24.7.1 or later,

  #3163 opened 2 months ago by tito-abbo
  5

• Callbacks from DAG .execute_workflow() needed for progress bar

  #3151 opened 2 months ago by peterjc
  4

• Running Snakemake --touch gives PulpSolverError

  #3128 opened 2 months ago by tbenavi1
  4

• Running Snakemake with slurm executor returns AttributeError

  #3179 opened 2 months ago by ericxytong
  1

• Helper function for turning Python filenames into module names (or vice versa)

  #3177 opened 2 months ago by edbennett
  0

• How to force Snakemake to run a rule only after all instances of a previous rule has finished

  #3160 opened 2 months ago by mgils4
  1

• Clarify default behavior of snakemake without "--cores" option

  #3167 opened 2 months ago by fhg-isi
  0

• Restoring cached folders results in a clock skew error

  #3097 opened 3 months ago by karl-az
  2

• Check for updated inputs while executing DAG

  #3161 opened 2 months ago by WeatherGod
  1

• Enhance Report Plugin Flexibility: Template Language Support, File Rendering Options, and Report Structure Customization

  #3102 opened 3 months ago by MatthiasLienhard
  3

• Announcement: Snakemake hackathon 2025 at CERN, call for participants!

  #3123 opened 3 months ago by johanneskoester
  1

• Sequential execution in one script of parallely defined rules.

  #3143 opened 2 months ago by gatoniel
  0

• Remove temporary paramiko version constraint

  #3120 opened 3 months ago by coderabbitai
  1

• `run` directive will reinitialize the global variables

  #3130 opened 2 months ago by jiangyun-fun
  2

• Question: Can you make an execute a snakemake workflow in pure python?

  #3136 opened 2 months ago by harrymatthews50
  0

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

  #3118 opened 3 months ago by tesujimath
  1

• Support standard Python virtual env. for rules

  #3124 opened 3 months ago by ccoulombe
  0

• Remove temporary paramiko version constraint

  #3119 opened 3 months ago by coderabbitai
  0

• snakemake dependency 'datrie' requires fragile C extention compiles on modern python

  #3105 opened 3 months ago by samimia-swks
  1

• Be able to depend on individual dataset(s) within an HDF5 file

  #3106 opened 3 months ago by edbennett
  0

• snakemake slurm seem to limit number of threads

  #3092 opened 3 months ago by benjamin-lieser
  6

• Rerun triggers not causing dependent steps to be rerun

  #3095 opened 3 months ago by powelleric
  4

• Snakemake output prints sensitive information with storage plugin

  #3087 opened 3 months ago by MattMonk
  1

• Conda + container fails to forward apptainer-args

  #3088 opened 3 months ago by karl-az
  0

• Visually group modules into single rules via `--modulegraph`

  #3086 opened 3 months ago by irm-codebase
  1