common-workflow-language/cwltool

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Common Workflow Language reference implementation

Stars: 376
Forks: 255
Open beginner issues: 0
Indexed issues: 451
Avg merge: 2d 7h
Merged PRs (30d): 12

Dominant language: Python
License: Apache-2.0
Last GitHub push: Sep 14, 2026
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted good first issue

Open All

451 open issues indexed

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

common-workflow-language/cwltool#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add requirements.txt and .python-version to root Open

common-workflow-language/cwltool#5 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
augment DOT/graphviz output Open

common-workflow-language/cwltool#7 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CWLtool issue with passing a list of scatter/gathered outputs into a program that accepts a list Open

common-workflow-language/cwltool#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CreateFileRequirement: input_dir and work_dir are the same Open

common-workflow-language/cwltool#21 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Validation error... could not validate field `secondaryFiles` Open

common-workflow-language/cwltool#23 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
dockerFile Open

status/awaiting user response

common-workflow-language/cwltool#26 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
No copyright declared in source code Open

common-workflow-language/cwltool#35 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
"No such file or directory" in very simple example Open

common-workflow-language/cwltool#45 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
--update should produce yaml if given yaml Open

enhancement

common-workflow-language/cwltool#51 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Symlinking input to docker on Mac links in local, not the host VM Open

common-workflow-language/cwltool#55 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`Error collecting output` for array of secondaryFiles Open

common-workflow-language/cwltool#57 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
inconsistent behavior: passing file paths via command line arguments vs input job documents Open

common-workflow-language/cwltool#79 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Using --cachedir option leaves output of workflow in cache instead of the directory the workflow is run Open

common-workflow-language/cwltool#86 · 7 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
content-type for remote descriptors Open

common-workflow-language/cwltool#98 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
output yaml instead of json Open

common-workflow-language/cwltool#109 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
test false negative with SoftwareRequirement Open

common-workflow-language/cwltool#120 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
InitialWorkDirRequirement `Error collecting output` when using DockerRequirement Open

common-workflow-language/cwltool#126 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
--leave-tmpdir doesn't work Open

common-workflow-language/cwltool#129 · 3 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
New cwltool error on basic gzip job Open

common-workflow-language/cwltool#130 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Lack of OS X testing Open

OSX

common-workflow-language/cwltool#138 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
document how to pass lists on the command line Open

common-workflow-language/cwltool#139 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
re-think continuous deployment model Open

common-workflow-language/cwltool#141 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Files in InitialWorkDir should have path in outdir Open

common-workflow-language/cwltool#146 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
--tool-help silently fails if parser can't be autogenerated Open

common-workflow-language/cwltool#152 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Auto-casting single item to array fails Open

common-workflow-language/cwltool#171 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
transient UTF parsing errors Open

common-workflow-language/cwltool#172 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
rerunning workflows with --cachedir sometimes repeats steps despite no changes to input Open

common-workflow-language/cwltool#173 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
docker volume on docker-machine Open

common-workflow-language/cwltool#179 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
cwltool requires type field on Process inputs contrary to the spec Open

common-workflow-language/cwltool#186 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
import directives not followed in input job objects if cwl:tool is used Open

bug help wanted

common-workflow-language/cwltool#188 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Problems with --cachedir and DockerRequirement Open

common-workflow-language/cwltool#203 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Error with --outdir Open

common-workflow-language/cwltool#205 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
attempts to write to /var/lib/cwl with docker hint but no docker installed Open

bug

common-workflow-language/cwltool#213 · 21 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add flag to ignore file formats Open

common-workflow-language/cwltool#217 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
enable use inside Jupyter notebooks Open

enhancement

common-workflow-language/cwltool#221 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
anonymous directory are allowed to only have a listing Open

common-workflow-language/cwltool#226 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
InitialWorkDir listing with expression returning a directory: TypeError Open

common-workflow-language/cwltool#227 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
cwltool does not recognize the array property 'length' in ECMAScript expressions Open

common-workflow-language/cwltool#235 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ExpressionTool cannot return one of its input files as an output Open

common-workflow-language/cwltool#248 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
better error message when InitialWorkDir listing is a single entry instead of an array Open

common-workflow-language/cwltool#249 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
doc_loader does not pickle correctly Open

common-workflow-language/cwltool#259 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
document what --basedir does Open

common-workflow-language/cwltool#278 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Unhandled exception when scattering over a Directory.listing Open

common-workflow-language/cwltool#279 · 5 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
OS X + docker under hints = permission error? Open

OSX

common-workflow-language/cwltool#281 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
flagging a input Directory as writable still symlinks all files, not copy Open

common-workflow-language/cwltool#282 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add additional code checks to automated testing Open

common-workflow-language/cwltool#286 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
document docker layout assumptions Open

common-workflow-language/cwltool#289 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
document that docker-in-virtualbox using shared folders doesn't work Open

common-workflow-language/cwltool#290 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Better Error message when cwl.output.json is invalid Open

help wanted

common-workflow-language/cwltool#291 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026

common-workflow-language/cwltool

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