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common-workflow-language

21 repository indicizzati · Vedi su GitHub

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

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

Python · 376 stelle
schema_salad
Semantic Annotations for Linked Avro Data

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

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

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

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

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

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

20 stelle
cwltest
Framework for testing CWL tools and workflows

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

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

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

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

Python · 7 stelle
cwl-v1.3

Common Workflow Language · 6 stelle
media
CWL logo source

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

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

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

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

1 stella
1 altro repository si trova su Vedi su GitHub

Aperta Tutte

1096 issue indicizzate finora

Exact definition of --tmp-outdir-prefix and --tmpdir-prefix is ambiguous Aperta

common-workflow-language/cwltool#3 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Add requirements.txt and .python-version to root Aperta

common-workflow-language/cwltool#5 · 4 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
augment DOT/graphviz output Aperta

common-workflow-language/cwltool#7 · 3 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
CWLtool issue with passing a list of scatter/gathered outputs into a program that accepts a list Aperta

common-workflow-language/cwltool#17 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
CreateFileRequirement: input_dir and work_dir are the same Aperta

common-workflow-language/cwltool#21 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Validation error... could not validate field `secondaryFiles` Aperta

common-workflow-language/cwltool#23 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
dockerFile Aperta

status/awaiting user response

common-workflow-language/cwltool#26 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
No copyright declared in source code Aperta

common-workflow-language/cwltool#35 · 4 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
"No such file or directory" in very simple example Aperta

common-workflow-language/cwltool#45 · 4 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
--update should produce yaml if given yaml Aperta

enhancement

common-workflow-language/cwltool#51 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Symlinking input to docker on Mac links in local, not the host VM Aperta

common-workflow-language/cwltool#55 · 4 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
`Error collecting output` for array of secondaryFiles Aperta

common-workflow-language/cwltool#57 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
inconsistent behavior: passing file paths via command line arguments vs input job documents Aperta

common-workflow-language/cwltool#79 · 1 commento · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Using --cachedir option leaves output of workflow in cache instead of the directory the workflow is run Aperta

common-workflow-language/cwltool#86 · 7 commenti · 1 reazione · 0 assegnatari · Indicizzata il 15/9/2026
content-type for remote descriptors Aperta

common-workflow-language/cwltool#98 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
output yaml instead of json Aperta

common-workflow-language/cwltool#109 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
test false negative with SoftwareRequirement Aperta

common-workflow-language/cwltool#120 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
InitialWorkDirRequirement `Error collecting output` when using DockerRequirement Aperta

common-workflow-language/cwltool#126 · 4 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
--leave-tmpdir doesn't work Aperta

common-workflow-language/cwltool#129 · 3 commenti · 1 reazione · 0 assegnatari · Indicizzata il 15/9/2026
New cwltool error on basic gzip job Aperta

common-workflow-language/cwltool#130 · 0 commenti · 0 reazioni · 1 assegnatario · Indicizzata il 15/9/2026
Lack of OS X testing Aperta

OSX

common-workflow-language/cwltool#138 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
document how to pass lists on the command line Aperta

common-workflow-language/cwltool#139 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
re-think continuous deployment model Aperta

common-workflow-language/cwltool#141 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Files in InitialWorkDir should have path in outdir Aperta

common-workflow-language/cwltool#146 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
--tool-help silently fails if parser can't be autogenerated Aperta

common-workflow-language/cwltool#152 · 1 commento · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Auto-casting single item to array fails Aperta

common-workflow-language/cwltool#171 · 5 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
transient UTF parsing errors Aperta

common-workflow-language/cwltool#172 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
rerunning workflows with --cachedir sometimes repeats steps despite no changes to input Aperta

common-workflow-language/cwltool#173 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
docker volume on docker-machine Aperta

common-workflow-language/cwltool#179 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
cwltool requires type field on Process inputs contrary to the spec Aperta

common-workflow-language/cwltool#186 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
import directives not followed in input job objects if cwl:tool is used Aperta

bug help wanted

common-workflow-language/cwltool#188 · 0 commenti · 1 reazione · 0 assegnatari · Indicizzata il 15/9/2026
Problems with --cachedir and DockerRequirement Aperta

common-workflow-language/cwltool#203 · 1 commento · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Error with --outdir Aperta

common-workflow-language/cwltool#205 · 7 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
attempts to write to /var/lib/cwl with docker hint but no docker installed Aperta

bug

common-workflow-language/cwltool#213 · 21 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
add flag to ignore file formats Aperta

common-workflow-language/cwltool#217 · 0 commenti · 1 reazione · 0 assegnatari · Indicizzata il 15/9/2026
enable use inside Jupyter notebooks Aperta

enhancement

common-workflow-language/cwltool#221 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
anonymous directory are allowed to only have a listing Aperta

common-workflow-language/cwltool#226 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
InitialWorkDir listing with expression returning a directory: TypeError Aperta

common-workflow-language/cwltool#227 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
cwltool does not recognize the array property 'length' in ECMAScript expressions Aperta

common-workflow-language/cwltool#235 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
ExpressionTool cannot return one of its input files as an output Aperta

common-workflow-language/cwltool#248 · 2 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
better error message when InitialWorkDir listing is a single entry instead of an array Aperta

common-workflow-language/cwltool#249 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
doc_loader does not pickle correctly Aperta

common-workflow-language/cwltool#259 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
document what --basedir does Aperta

common-workflow-language/cwltool#278 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Unhandled exception when scattering over a Directory.listing Aperta

common-workflow-language/cwltool#279 · 5 commenti · 1 reazione · 0 assegnatari · Indicizzata il 15/9/2026
OS X + docker under hints = permission error? Aperta

OSX

common-workflow-language/cwltool#281 · 1 commento · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
flagging a input Directory as writable still symlinks all files, not copy Aperta

common-workflow-language/cwltool#282 · 9 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
add additional code checks to automated testing Aperta

common-workflow-language/cwltool#286 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
document docker layout assumptions Aperta

common-workflow-language/cwltool#289 · 2 commenti · 0 reazioni · 1 assegnatario · Indicizzata il 15/9/2026
document that docker-in-virtualbox using shared folders doesn't work Aperta

common-workflow-language/cwltool#290 · 0 commenti · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026
Better Error message when cwl.output.json is invalid Aperta

help wanted

common-workflow-language/cwltool#291 · 1 commento · 0 reazioni · 0 assegnatari · Indicizzata il 15/9/2026

common-workflow-language

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