Owner

common-workflow-language

21 indexed repositories · View on GitHub

common-workflow-language
Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Common Workflow Language · 1480 stars
cwltool
Common Workflow Language reference implementation

Python · 376 stars
schema_salad
Semantic Annotations for Linked Avro Data

Python · 86 stars
cwlviewer
A web application to view and share Common Workflow Language workflows

Java · 52 stars
cwl-v1.2
Released CWL v1.2.1 specification

Common Workflow Language · 45 stars
cwl-utils
Python utilities for CWL

Python · 43 stars
user_guide
The CWL v1.0 - v1.2 user guide

Common Workflow Language · 42 stars
workflow-service
Implementation of the GA4GH Workflow Execution Service, a REST service for running workflows

Python · 39 stars
cwlprov
Profile for provenance research object of a CWL workflow run

20 stars
cwltest
Framework for testing CWL tools and workflows

Python · 20 stars
cwljava
Java SDK for the Common Workflow Language standards

Java · 16 stars
cwl-website
www.commonwl.org

JavaScript · 10 stars
cwl-intro-gui-workshop
Materials to teach workshop about CWL using the Rabix Composer

Common Workflow Language · 8 stars
cwl-upgrader
Upgrade CWL syntax to a newer version

Python · 7 stars
cwl-v1.3

Common Workflow Language · 6 stars
media
CWL logo source

5 stars
governance
Holds public material generated by and for the CWL board.

HTML · 4 stars
cwlprov-py
cwlprov: Command line tool and Python API to explore Research Objects containing provenance of Common Workflow Language executions

Python · 4 stars
for_novices
One page CWL explainer for workflow novices

1 star
for_decision_makers
One page CWL explainer for Business/policy decision makers

1 star
1 more repository lives on View on GitHub

Open All

1096 open issues indexed

Error if prefix is absent Open

status/awaiting user response

common-workflow-language/cwltool#298 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
re-work to better follow the CWL user guide Open

common-workflow-language/cwl-intro-gui-workshop#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Hands on #1 uses an invalid File object. Open

common-workflow-language/cwl-intro-gui-workshop#2 · 2 comments · 1 reaction · 1 assignee · Indexed Sep 15, 2026
Hands on codes and files moves to this repository Open

common-workflow-language/cwl-intro-gui-workshop#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Change scatter/gather example to use better names Open

common-workflow-language/cwl-intro-gui-workshop#4 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Test auto merge feature Open

common-workflow-language/cwl-intro-gui-workshop#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Failed confirmation test on OSX Open

common-workflow-language/cwltool#302 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
KeyError: 'location' - Cannot make job: 'location' Open

common-workflow-language/cwltool#303 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Initializes job assuming Docker is available, still tries to run it if not Open

common-workflow-language/cwltool#304 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Type mismatch between source and sink when using merge_nested for single-item list of input link Open

common-workflow-language/cwltool#309 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Can't 'add' files to a docker container Open

common-workflow-language/cwltool#312 · 10 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
support plugins for third party CWL registry APIs, etc Open

common-workflow-language/cwltool#314 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
conform to the spec: paths for File and Directory inputs placed in the InitialWorkDir must reflect that location and no other Open

common-workflow-language/cwltool#325 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Docker mount problem on MAC Open

OSX

common-workflow-language/cwltool#328 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Cwltool doesn't recognise syntax sugar for array of arrays Open

common-workflow-language/cwltool#330 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
jobs exceeding max allocation of a resource are not limited or failed Open

common-workflow-language/cwltool#339 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
specifying float or int inputs on command line to cwltool doesn't work Open

common-workflow-language/cwltool#342 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
no html5lib? print useful warning, don't fail Open

common-workflow-language/cwltool#347 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Docker: directory mount fails Open

common-workflow-language/cwltool#355 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
support mutually exclusive parameters specification on the command line Open

common-workflow-language/cwltool#358 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
TES backend? Open

common-workflow-language/cwltool#359 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Problem with Directory output Open

common-workflow-language/cwltool#361 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
should use both `doc` and `label` when generating CLI for a CWL description Open

common-workflow-language/cwltool#362 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Logging all information of a session in a log file for easy understanding by developers in case of a issue Open

common-workflow-language/cwltool#364 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Typos in parameters give unhelpful errors Open

bug

common-workflow-language/cwltool#370 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
bad user experience if an array is provided to a File's path Open

common-workflow-language/cwltool#372 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Different behavior when "valueFrom" is absent and when it's "null" Open

common-workflow-language/cwltool#373 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Missing Basename when using current directory as an input Open

common-workflow-language/cwltool#376 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
unable to parse type: long as input through cli Open

common-workflow-language/cwltool#385 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
auto guess format for File types when receiving inputs on the command line instead of an input object, Open

common-workflow-language/cwltool#389 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
parameter references should be removed from cache hash calculations Open

common-workflow-language/cwltool#395 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`--validate` should validate parameter references Open

common-workflow-language/cwltool#398 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Bad interpreting of Null Open

common-workflow-language/cwltool#405 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Wrong rdfs namespace in cwltool --print-rdf Open

common-workflow-language/cwltool#427 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
cwl:cwlVersion in RDF output has incorrect base URL Open

common-workflow-language/cwltool#429 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
static_checker mistakenly fails with source -> sink Open

common-workflow-language/cwltool#437 · 0 comments · 2 reactions · 0 assignees · Indexed Sep 15, 2026
Valid workflow cannot have RDF generated due to lack of urlencoding Open

common-workflow-language/cwltool#444 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Difference in optional arguments handling using .yml config and manually provided paramters Open

common-workflow-language/cwltool#446 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
accept globs using the CLI interface for inputs that are File[] or Directory Open

enhancement good first issue gsoc help wanted

common-workflow-language/cwltool#448 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
support secondaryFiles for File in CommandInputRecordField Open

common-workflow-language/cwltool#480 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
cwl-runner re-executes cached jobs Open

common-workflow-language/cwltool#493 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 15, 2026
new PR tester needed: run conformance tests with Toil using changes Open

common-workflow-language/cwltool#502 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
munge spaces when generating CLI interface Open

common-workflow-language/cwltool#515 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enhance --pack to replace default Files with File literals? Open

common-workflow-language/cwltool#531 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
--no-container & --cachedir combo produce an error Open

bug good first issue help wanted

common-workflow-language/cwltool#537 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Feature request: set secondaryFiles in workflow step input Open

common-workflow-language/cwltool#538 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
using scattered value more than once in a step fails Open

common-workflow-language/cwltool#540 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
move non-standard command line options that change execution behavior to cwltool specific CWL extensions Open

common-workflow-language/cwltool#543 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Docker image for cwltool does not work on Docker v17.06.2-ce-mac27 Open

bug OSX

common-workflow-language/cwltool#546 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
AttributeError: 'NoneType' object has no attribute 'get' Open

common-workflow-language/cwltool#555 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026

common-workflow-language

Get new issues in your inbox