common-workflow-language cwltool issues

common-workflow-language / cwltool

Common Workflow Language reference implementation

https://www.commonwl.org

Apache License 2.0

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issues

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Update galaxy-util requirement from <24.1 to <24.2

#2015 dependabot[bot] closed 1 day ago
1
Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1,>=22.1.2 to !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,>=24.1.1,<24.2

#2014 dependabot[bot] closed 10 hours ago
2
[Snyk] Security upgrade python from 3.12-alpine3.17 to 3.13.0a2-alpine3.17

#2013 mr-c closed 3 days ago
1
Use uv compatible syntax in test-requirements.txt

#2012 hauntsaninja closed 3 days ago
1
Bump docker/build-push-action from 5 to 6

#2011 ElderMedic closed 1 week ago
1
Fix 2d output arrays with format tag

#2010 vjaganat90 opened 1 week ago
1
Bump mypy from 1.10.0 to 1.10.1

#2009 dependabot[bot] closed 1 day ago
1
Bump docker/build-push-action from 5 to 6

#2008 dependabot[bot] closed 2 weeks ago
1
Confusing provenance model (`wasStartedBy`/`qualifiedStart`/`wasEndedBy`/`qualifiedEnd`)

#2007 avillar opened 1 month ago
0
Added new loop test

#2006 LanderOtto opened 1 month ago
1
bump prov to 2.0.1

#2005 jfennick opened 1 month ago
3
Update branch to sync with main

#2004 ElderMedic closed 1 month ago
0
flaky conformance test with `cwltool`: simple_simple_scatter

#2003 mr-c opened 1 month ago
0
Add docstrings to functions in `ro.py`

#2002 AGoetzee closed 1 month ago
2
Workflows with `DockerRequirement` fail when using Podman 5.0.2

#2001 tom-tan opened 1 month ago
1
--debug should print the URL of the downloading schema

#2000 inutano opened 1 month ago
0
Evaluation expressions that timeout can raise JSONDecodeError

#1999 brettcs opened 1 month ago
0
Replace .decode method with str(bytes, "utf-8")

#1998 tetron closed 2 months ago
2
build now uses the module name

#1997 mr-c closed 2 months ago
1
Update pytest requirement from <8.2,>=6.2 to >=6.2,<8.3

#1996 dependabot[bot] closed 2 months ago
2
Bump mypy from 1.9.0 to 1.10.0

#1995 dependabot[bot] closed 1 month ago
2
Update flake8-bugbear requirement from <24.3 to <24.5

#1994 dependabot[bot] opened 2 months ago
2
Update paths for the CWL v1.2 conformance tests now that 1.2.1 has been released.

#1993 mr-c closed 2 months ago
1
Update black requirement from ~=24.3 to ~=24.4

#1992 dependabot[bot] closed 1 month ago
4
podman nor singularity/apptainer support is experimental

#1991 mr-c closed 3 months ago
0
Galaxy-* 24.0.0

#1990 mr-c closed 3 months ago
1
Prov data input output

#1989 mr-c opened 3 months ago
2
Update galaxy-util requirement from <23.2 to <24.1

#1988 dependabot[bot] closed 3 months ago
2
Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.3,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1

#1987 dependabot[bot] closed 3 months ago
2
Update and Check loadListing for input dir provenance

#1986 ElderMedic closed 3 months ago
1
Update black requirement from ~=24.2 to ~=24.3

#1985 dependabot[bot] closed 3 months ago
1
pytest: use the worksteal scheduler and run on all logical cores, not just physical.

#1984 mr-c closed 3 months ago
1
biocontainers test is flaky, automatically retry it.

#1983 mr-c closed 3 months ago
1
Bump mypy from 1.8.0 to 1.9.0

#1982 dependabot[bot] closed 3 months ago
1
setuptools: silence package discovery warnings

#1981 mr-c closed 3 months ago
1
Update pytest requirement from <8.1,>=6.2 to >=6.2,<8.2

#1980 dependabot[bot] closed 4 months ago
1
patch dockerFile build

#1979 misterbrandonwalker closed 1 month ago
3
Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.2,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.3

#1978 dependabot[bot] closed 4 months ago
1
Append "cwltool" to HTTP User-Agent string

#1977 svonworl closed 4 months ago
4
Update black requirement from ~=24.1 to ~=24.2

#1976 dependabot[bot] closed 4 months ago
1
Update flake8-bugbear requirement from <24.2 to <24.3

#1975 dependabot[bot] closed 4 months ago
1
Adding new choice to --on-error

#1974 AlexTate opened 5 months ago
2
Bump codecov/codecov-action from 3 to 4

#1973 dependabot[bot] closed 5 months ago
1
add the --shm-size parameter at runtime

#1972 lihl2014 closed 5 months ago
4
Update pytest requirement from <7.5,>=6.2 to >=6.2,<8.1

#1971 dependabot[bot] closed 5 months ago
1
Update black requirement from ~=23.12 to ~=24.1

#1970 dependabot[bot] closed 5 months ago
1
CWL Conditionals, when component doesn't handle condition when tool input parameter is a non-optional file with loadContents set to true

#1969 alexiswl opened 5 months ago
2
Bump actions/cache from 3 to 4

#1968 dependabot[bot] closed 5 months ago
1
Add CITATION.cff / codemeta.json file

#1967 mr-c opened 5 months ago
0
Update flake8-bugbear requirement from <23.13 to <24.2

#1966 dependabot[bot] closed 5 months ago
1