common-workflow-language / cwl-utils

Python utilities for CWL

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

common-workflow-language/cwl-utils Issues

ruamel.yaml doesn't support yaml.dump()
Updated 3 months ago1
cwl-graph-split causes some odd errors for a packed pipeline
Updated 3 months ago
Proposal for a Function to Generate JSON Schema for Workflow Parameter Files
Updated 4 months ago3
Inconsistent `type` attribute in `CommandInputParameter`
Updated 5 months ago
New tests needed to catch future regressions
Updated 6 months ago
pack command fails on complex workflow with error 'MissingTypeName'
Closed a year ago5
Reading a packed workflow returns only the Workflow object
Closed a year ago1
test & support apptainer in addition to singularity-ce
Updated a year ago
Using node:slim container hitting Docker pull rate limit
Closed 2 years ago
Create conda package
Closed 2 years ago2
Crash when reading ML prediction workflow
Closed 2 years ago2
test __eq__ & __hash__ with load/save of all CWL conformance tests
Updated 2 years ago
add utilities to help with parsing CWL Parameter References
Updated 2 years ago
new feature: implement cwltool --pack
Closed 2 years ago
switching to all Apache 2.0 licensing
Closed 2 years ago8
docker_extract.py is not handling relative directories very well.
Updated 2 years ago1
Fix https://cwl-utils.readthedocs.io/
Updated 2 years ago7
[Feature Request] utility function to access nested fields
Updated 2 years ago1
TypeError: 'NoneType' object is not callable in NodeJSEngine.__del__()
Updated 2 years ago
Question: Convert v1.0 to v1.2
Closed 3 years ago7
Cannot execute the import statement of example in `README.md`.
Closed 3 years ago3
The required of `SecondaryFileSchema` is set to `None`
Closed 3 years ago1
A packed object with `$graph` can be loaded via `load_document_by_yaml` but the loaded object cannot be saved as the packed object
Closed 3 years ago2
Feature request: provide a way to convert CWL objects to a dictionary
Closed 3 years ago4
Documentation for importing packed files
Updated 3 years ago10
InputArraySchema can't find some types
Closed 3 years ago
Importing tools that use `SchemaDefRequirement` requires schema to be present in $namespaces
Closed 3 years ago1
test on python 3.8 and 3.9
Closed 3 years ago1
new feature: implement cwltool --target / --single-{step,process} --print-{subgraph,target}
Updated 3 years ago
Subtree of workflow is updated only to v1.1
Updated 3 years ago
single script CWL normalizer
Closed 3 years ago
Create example of creating a CWL document from scratch
Closed 3 years ago1
Change license to Apache 2.0
Closed 3 years ago
document release process
Updated 3 years ago3
AttributeError: 'CommentedMap' object has no attribute 'decode'
Closed 3 years ago4
remaining issues for the CWL Expression extractor/transformer
Closed 3 years ago1
expr refactor new feature: consolidate generated `ExpressionTool`/`CommandLineTool`s
Updated 3 years ago
expr refactor: download conformance tests and process & run them
Updated 3 years ago
cwlgen export functionality
Closed 3 years ago1
expr refactor: quoting in generated javascript is sometimes wrong
Closed 4 years ago4
Slow document loading starting with 0.3
Closed 4 years ago2
expr refactor: pickValue on a Workflow step input
Updated 4 years ago
schema_salad.exceptions.ValidationExceptions parsing certain data structures
Updated 4 years ago12
newer parsers choking on secondaryFiles input
Closed 4 years ago1
container image puller: consider using https://github.com/biowdl/prepull-singularity
Updated 4 years ago
Dependabot couldn't authenticate with https://pypi.python.org/simple/
Closed 4 years ago
load_document fails with $schemas field?
Closed 4 years ago2
ImportError: cannot import name 'Fetcher' from 'schema_salad.ref_resolver'
Closed 4 years ago1
Request: tool to replace simple docker references with digests
Updated 4 years ago4
New release of cwl-utils
Closed 4 years ago5