common-workflow-language

common-workflow-language/cwl-utils

Python utilities for CWL

Stars: 43
Forks: 28
Open beginner issues: 0
Indexed issues: 25
Avg merge: 4h 7m
Merged PRs (30d): 4

Dominant language: Python
License: Apache-2.0
Last GitHub push: Sep 7, 2026
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue help wanted

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25 open issues indexed

types for input/output not consistent Open

common-workflow-language/cwl-utils#2 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
teach cite_extract to generate a bibtex ".bib" bibliography Open

enhancement good first issue help wanted

common-workflow-language/cwl-utils#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Request: tool to replace simple docker references with digests Open

common-workflow-language/cwl-utils#19 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
document release process Open

common-workflow-language/cwl-utils#22 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
schema_salad.exceptions.ValidationExceptions parsing certain data structures Open

common-workflow-language/cwl-utils#31 · 12 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
container image puller: consider using https://github.com/biowdl/prepull-singularity Open

common-workflow-language/cwl-utils#35 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
expr refactor: pickValue on a Workflow step input Open

common-workflow-language/cwl-utils#44 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
expr refactor: download conformance tests and process & run them Open

common-workflow-language/cwl-utils#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
expr refactor new feature: consolidate generated `ExpressionTool`/`CommandLineTool`s Open

common-workflow-language/cwl-utils#49 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix https://cwl-utils.readthedocs.io/ Open

common-workflow-language/cwl-utils#57 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Documentation for importing packed files Open

common-workflow-language/cwl-utils#71 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Subtree of workflow is updated only to v1.1 Open

common-workflow-language/cwl-utils#89 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
new feature: implement cwltool --target / --single-{step,process} --print-{subgraph,target} Open

common-workflow-language/cwl-utils#92 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
[Feature Request] utility function to access nested fields Open

common-workflow-language/cwl-utils#106 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
docker_extract.py is not handling relative directories very well. Open

common-workflow-language/cwl-utils#157 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add utilities to help with parsing CWL Parameter References Open

common-workflow-language/cwl-utils#162 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
test __eq__ & __hash__ with load/save of all CWL conformance tests Open

common-workflow-language/cwl-utils#168 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
test & support apptainer in addition to singularity-ce Open

common-workflow-language/cwl-utils#185 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
New tests needed to catch future regressions Open

common-workflow-language/cwl-utils#260 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Inconsistent `type` attribute in `CommandInputParameter` Open

common-workflow-language/cwl-utils#271 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Proposal for a Function to Generate JSON Schema for Workflow Parameter Files Open

common-workflow-language/cwl-utils#273 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
new command: cwl-summary Open

common-workflow-language/cwl-utils#314 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CWL steps given in alphabetical order rather than the order in the CWL file Open

common-workflow-language/cwl-utils#326 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Issue with Docker tag handling Open

common-workflow-language/cwl-utils#339 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
'save' function truncate input source name if it contains step name Open

common-workflow-language/cwl-utils#402 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026

A short digest of beginner-friendly GitHub issues.