common-workflow-language/cwl-utils

Issues

• CWL steps given in alphabetical order rather than the order in the CWL file

  #326 opened 3 months ago by Ambivalentalfa
  0

• new command: cwl-summary

  #314 opened 5 months ago by mr-c
  0

• Parser does not support cwltool extensions

  #309 opened 6 months ago by stxue1
  0

• ruamel.yaml doesn't support yaml.dump()

  #285 opened a year ago by alexiswl
  1

• cwl-graph-split causes some odd errors for a packed pipeline

  #286 opened a year ago by alexiswl
  0

• Proposal for a Function to Generate JSON Schema for Workflow Parameter Files

  #273 opened a year ago by suecharo
  3

• Inconsistent `type` attribute in `CommandInputParameter`

  #271 opened a year ago by camilovelezr
  0

• New tests needed to catch future regressions

  #260 opened a year ago by mr-c
  0

• pack command fails on complex workflow with error 'MissingTypeName'

  #220 opened 2 years ago by alexiswl
  5

• Reading a packed workflow returns only the Workflow object

  #200 opened 2 years ago by simleo
  1

• test & support apptainer in addition to singularity-ce

  #185 opened 2 years ago by mr-c
  0

• Using node:slim container hitting Docker pull rate limit

  #177 opened 2 years ago by adrabent
  0

• Create conda package

  #138 opened 2 years ago by kinow
  2

• Crash when reading ML prediction workflow

  #175 opened 2 years ago by simleo
  2

• test __eq__ & __hash__ with load/save of all CWL conformance tests

  #168 opened 2 years ago by mr-c
  0

• add utilities to help with parsing CWL Parameter References

  #162 opened 2 years ago by mr-c
  0

• new feature: implement cwltool --pack

  #91 opened 2 years ago by mr-c
  0

• switching to all Apache 2.0 licensing

  #155 opened 2 years ago by mr-c
  8

• docker_extract.py is not handling relative directories very well.

  #157 opened 2 years ago by golharam
  1

• Fix https://cwl-utils.readthedocs.io/

  #57 opened 4 years ago by nyue
  7

• [Feature Request] utility function to access nested fields

  #106 opened 3 years ago by tom-tan
  1

• TypeError: 'NoneType' object is not callable in NodeJSEngine.__del__()

  #137 opened 2 years ago by mr-c
  0

• Question: Convert v1.0 to v1.2

  #88 opened 3 years ago by BJWiley233
  7

• Cannot execute the import statement of example in `README.md`.

  #108 opened 3 years ago by suecharo
  3

• The required of `SecondaryFileSchema` is set to `None`

  #113 opened 3 years ago by suecharo
  1

• A packed object with `$graph` can be loaded via `load_document_by_yaml` but the loaded object cannot be saved as the packed object

  #98 opened 3 years ago by tom-tan
  2

• Feature request: provide a way to convert CWL objects to a dictionary

  #97 opened 3 years ago by tom-tan
  4

• Documentation for importing packed files

  #71 opened 4 years ago by alexiswl
  10

• InputArraySchema can't find some types

  #93 opened 3 years ago by mr-c
  0

• Importing tools that use `SchemaDefRequirement` requires schema to be present in $namespaces

  #74 opened 3 years ago by alexiswl
  1

• test on python 3.8 and 3.9

  #23 opened 3 years ago by mr-c
  1

• new feature: implement cwltool --target / --single-{step,process} --print-{subgraph,target}

  #92 opened 3 years ago by mr-c
  0

• Subtree of workflow is updated only to v1.1

  #89 opened 3 years ago by BJWiley233
  0

• single script CWL normalizer

  #56 opened 4 years ago by mr-c
  0

• Create example of creating a CWL document from scratch

  #68 opened 4 years ago by mr-c
  1

• Change license to Apache 2.0

  #58 opened 4 years ago by mr-c
  0

• document release process

  #22 opened 5 years ago by mr-c
  3

• expr refactor new feature: consolidate generated `ExpressionTool`/`CommandLineTool`s

  #49 opened 4 years ago by mr-c
  0

• expr refactor: download conformance tests and process & run them

  #45 opened 4 years ago by mr-c
  0

• cwlgen export functionality

  #33 opened 4 years ago by JoanaFMorgado
  1

• expr refactor: quoting in generated javascript is sometimes wrong

  #46 opened 4 years ago by mr-c
  4

• Slow document loading starting with 0.3

  #34 opened 4 years ago by ksebby
  2

• expr refactor: pickValue on a Workflow step input

  #44 opened 4 years ago by mr-c
  0

• schema_salad.exceptions.ValidationExceptions parsing certain data structures

  #31 opened 4 years ago by leipzig
  12

• newer parsers choking on secondaryFiles input

  #39 opened 4 years ago by leipzig
  1

• container image puller: consider using https://github.com/biowdl/prepull-singularity

  #35 opened 4 years ago by mr-c
  0

• Dependabot couldn't authenticate with https://pypi.python.org/simple/

  #32 opened 4 years ago by dependabot-preview
  0

• load_document fails with $schemas field?

  #25 opened 4 years ago by leipzig
  2

• ImportError: cannot import name 'Fetcher' from 'schema_salad.ref_resolver'

  #20 opened 5 years ago by ryantanaka
  1

• Request: tool to replace simple docker references with digests

  #19 opened 5 years ago by mr-c
  4