DataBiosphere/toil

Issues

• Make a new Toil release

  #5191 opened 21 days ago by stxue1
  0

• Connect Toil CWL conformance CI to CWL project badge generation

  #5183 opened a month ago by unito-bot
  1

• Add filesize sniffing to specify the import job's disk space for WDL and CWL

  #5114 opened a month ago by stxue1
  2

• toil ignores LoadListingRequirement

  #5099 opened 4 months ago by adrabent
  8

• Cactus integration test on master branch is failing.

  #5184 opened a month ago by DailyDreaming
  0

• Python3.12 SyntaxWarning

  #5186 opened a month ago by tillea
  1

• Error message when job killed for running out of slurm time is very misleading

  #5177 opened a month ago by glennhickey
  1

• Cut AWS testing costs by 75%

  #5162 opened a month ago by unito-bot
  7

• Speed up CWL conformance tests to ~10 minutes total using the pytest plugin

  #5182 opened a month ago by unito-bot
  0

• Support multi-arch Singularity

  #5181 opened a month ago by unito-bot
  0

• Support mixed-arch HPC where leader and jobs need different Python interpreters

  #5180 opened a month ago by unito-bot
  0

• Add security context to Kubernetes batch system

  #5179 opened a month ago by xhejtman
  0

• Dependabot config is broken

  #5175 opened a month ago by adamnovak
  0

• Toil can complain that it can't import `missing:` protocol files, instead of that a particular user-supplied URL points to a missing file

  #5174 opened a month ago by adamnovak
  1

• Bug in overriding coordination_dir in toil/common.py

  #5152 opened a month ago by gmloose
  1

• workDir and jobStore should default to (shared) tmp-outdir-prefix

  #5143 opened a month ago by gmloose
  1

• Use real secret key management

  #5173 opened a month ago by unito-bot
  0

• Set up Gitlab to test PRs from other forks without needing to copy them in to ours

  #5172 opened a month ago by unito-bot
  0

• Support CWL tool version 1.3 .

  #5171 opened a month ago by DailyDreaming
  0

• Implement CWL loop extension

  #5169 opened 2 months ago by adamnovak
  1

• Add FTP support to `AbstractJobStore._get_size`

  #5134 opened 2 months ago by stxue1
  1

• WDL Docker stats support is not documented

  #5168 opened 2 months ago by adamnovak
  0

• Support FTP over SSL

  #5167 opened 2 months ago by stxue1
  0

• The defined --defaultMemory does not apply to CWL jobs without memory values and 256 is always used instead

  #5165 opened 2 months ago by ndonyapour
  2

• Generic Toil Utilities require cluster utilities

  #5164 opened 2 months ago by lonbar
  1

• Proper way to access local node paths in Toil, AWS Batch backend, for CWL workflows

  #5163 opened 2 months ago by robertbio
  1

• Send some metrics to QA Dockstore

  #5159 opened 2 months ago by unito-bot
  9

• Toil complains that a filename with spaces "contains illegal characters" while cwltool works fine

  #5158 opened 2 months ago by ndonyapour
  5

• Telemetry About Toil Usage

  #5160 opened 2 months ago by unito-bot
  1

• Toil User Surveys

  #5161 opened 2 months ago by unito-bot
  0

• toil-cwl-runner can ignore LoadListingRequirements on a Workflow and always uses `no_listing`

  #5104 opened 2 months ago by stxue1
  1

• Python3.8 has reached End of Life

  #5125 opened 2 months ago by DailyDreaming
  1

• Fix failing CWLWorkflowTest

  #5150 opened 2 months ago by gmloose
  2

• Upgrade to Python 3.13

  #5130 opened 2 months ago by stxue1
  0

• Reboot support for server mode

  #5148 opened 2 months ago by unito-bot
  0

• Make Slurm Docker images for CI testing

  #5147 opened 2 months ago by unito-bot
  0

• Add WDL unit tests to CI

  #5109 opened 2 months ago by stxue1
  0

• JobServiceTest.testServiceParallelRecursive can time out

  #5140 opened 3 months ago by adamnovak
  1

• Collision error when passing input as the output in toil-cwl-runner

  #5137 opened 2 months ago by stxue1
  0

• WDL has trouble with JSON file imports due to normalization

  #5120 opened 3 months ago by stxue1
  0

• Add leader import fallback to running imports on workers

  #5135 opened 3 months ago by stxue1
  0

• CI is failing due to a lint failure from merge

  #5106 opened 3 months ago by adamnovak
  1

• Add import on workers for WDL

  #5113 opened 3 months ago by adamnovak
  0

• toil partially incompatible with Python 3.13 due to removal of "pipes" from the standard library

  #5119 opened 3 months ago by mr-c
  1

• Fix flatcar test flakiness

  #5092 opened 3 months ago by DailyDreaming
  2

• Permission denied: 'amd-smi' - Error while detecting accelerators

  #5111 opened 3 months ago by ndonyapour
  4

• Add workaround for compatibility with WDL workflows that expect the user to have access to task-level outputs

  #5093 opened 3 months ago by adamnovak
  1

• When a WDL 1.0 workflow has no output section, task outputs don't make it out of the workflow if the calls are inside conditionals or scatters

  #5094 opened 3 months ago by adamnovak
  0

• `CachingFileStoreTestWithAwsJobStore.testSimultaneousReadsUncachedStream` is flaky

  #5097 opened 4 months ago by adamnovak
  0

• Toil resource monitoring will break `wait` in WDL scripts

  #5090 opened 4 months ago by adamnovak
  0