common-workflow-language

common-workflow-language/cwltool

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

Error message for numbers that should be strings in arguments could be clearer Open

common-workflow-language/cwltool#1009 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Recording timestamps in logging should be optional feature? Open

discussion

common-workflow-language/cwltool#1012 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Not indented namespace declaration error message is difficult to understand Open

common-workflow-language/cwltool#1013 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Docker on Mac problem when I execute test_iwdr.py::test_iwdr_permutations_inplace Open

common-workflow-language/cwltool#1018 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
GA4GH TRS: linked files fail to resolve Open

common-workflow-language/cwltool#1022 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 15, 2026
cwltool fails to emit error when ExpressionTool expression does not match expected output format Open

common-workflow-language/cwltool#1026 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
No easy way to pass false to a boolean parameter via the command line Open

common-workflow-language/cwltool#1030 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Workflow Factory should use argparse Open

common-workflow-language/cwltool#1031 · 0 comments · 2 reactions · 0 assignees · Indexed Sep 15, 2026
Stdout and Stderr are required for ComanndLine Option Open

common-workflow-language/cwltool#1032 · 3 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
tmp Dir exists already Open

common-workflow-language/cwltool#1036 · 7 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
ValidationException error due to incompatiblility Open

common-workflow-language/cwltool#1041 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Staging input files in a non-writable sub-directory fails on Linux Open

bug help wanted

common-workflow-language/cwltool#1042 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
writable secondaryFiles don't seem to work Open

common-workflow-language/cwltool#1046 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CWL with R returns empty output directory with "Final process status is success" status Open

common-workflow-language/cwltool#1050 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
cwltool:overrides: add an alias for any Process Open

common-workflow-language/cwltool#1052 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CWLtool scatter dot product is not scattering the steps and it is overwriting the output results Open

common-workflow-language/cwltool#1053 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Error collecting output for singularity jobs Open

common-workflow-language/cwltool#1054 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
tool dependency resolver with conda & scatter: not tested Open

common-workflow-language/cwltool#1057 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Record container id failed when a relative path is passed to --cidfile-dir Open

common-workflow-language/cwltool#1058 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Provenance can not be used with parallel Open

common-workflow-language/cwltool#1059 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
error with checker.py Open

common-workflow-language/cwltool#1062 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
too slow validating some packed workflows Open

common-workflow-language/cwltool#1063 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Parallel execution javascript evaluation error Open

common-workflow-language/cwltool#1065 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
need test for compute checksum regression Open

common-workflow-language/cwltool#1068 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
resolver.py failing to resolve a relative path Open

common-workflow-language/cwltool#1070 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
InitialWorkDirRequirement fails to create an empty listing.entryname file Open

common-workflow-language/cwltool#1076 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
regression: --pack, relative run references when loading from a URL Open

common-workflow-language/cwltool#1077 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
cwltool expects string for envDef Open

common-workflow-language/cwltool#1148 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Invalid filename if it contains # Open

common-workflow-language/cwltool#1083 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
--tmpdir-prefix is ignored Open

common-workflow-language/cwltool#1084 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
investigate lpmx as an additional rootless docker backed Open

common-workflow-language/cwltool#1085 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Investigate rootless containers using runc / umoci Open

discussion

common-workflow-language/cwltool#1086 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
stagedir not configurable, sometimes uses system tempory directory vs requested tmpdir Open

common-workflow-language/cwltool#1087 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
A Workflow with two steps of the same ExpressionTool fails if the tool inputs an array of files with loadContents Open

common-workflow-language/cwltool#1094 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Odd validation failures for valid document Open

common-workflow-language/cwltool#1096 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Output log formats for CommandLineTool and Workflow are (slightly) not consistent Open

common-workflow-language/cwltool#1100 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Behavior of `default` field of file and directory in CommandLineTool is strange Open

common-workflow-language/cwltool#1101 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
'--pack' option fails when '--validate' works fine Open

bug help wanted

common-workflow-language/cwltool#1103 · 1 comment · 4 reactions · 0 assignees · Indexed Sep 15, 2026
Logged memory usage should indicate it is from cwltool Open

common-workflow-language/cwltool#1108 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CWLtools throwing error upon usage of secondary files for capturing log files from star aligner on two different versions Open

common-workflow-language/cwltool#1110 · 8 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Can't return 0 for optional int/float output Open

common-workflow-language/cwltool#1121 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
"entry" content interpretation Open

common-workflow-language/cwltool#1124 · 4 comments · 4 reactions · 0 assignees · Indexed Sep 15, 2026
when downloading a remote File resource, display a message Open

common-workflow-language/cwltool#1125 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Errors are noisy on python3 Open

common-workflow-language/cwltool#1126 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Detect when Singularity isn't properly configured to mount local folders Open

common-workflow-language/cwltool#1144 · 15 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
WorkflowStep.{requirements,hints} are unable to see inputs that aren't apart of the WorkflowStep.run procces Open

common-workflow-language/cwltool#1147 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Secondary Files required Open

common-workflow-language/cwltool#1151 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Need better error message when type: File, but the glob returns many matches Open

common-workflow-language/cwltool#1160 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Argument with prefix = empty string and separate = false is omitted from cmd line Open

common-workflow-language/cwltool#1165 · 3 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Fuzzing cwltool Open

enhancement gsoc

common-workflow-language/cwltool#1170 · 14 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

A short digest of beginner-friendly GitHub issues.