Issues

• --provenance fails a successful run when two data files share a basename

  common-workflow-language/cwltool#2369 · Filter by author vjaganat90 opened on Oct 20, 2026

• cwltool fails to execute on Fugaku when launched with virtual environment from login node

  common-workflow-language/cwltool#2353 · Filter by author kinow opened on Sep 20, 2026
  5

• Invalid --pack results if input and output have the same name in a referred CWL

  common-workflow-language/cwltool#2343 · Filter by author EmileSonneveld opened on Aug 26, 2026

• Network namepaces "none" fails on machines/clusters without user namespaces

  common-workflow-language/cwltool#2337 · Filter by author tikk3r opened on Aug 18, 2026
  3

• --single-step <stepname> plus --help to list the inputs doesn't produce the correct results

  common-workflow-language/cwltool#2299 · Filter by author mr-c opened on Jul 2, 2026

• cwltool:MPIRequirement works without declaring the namespace cwltool

  common-workflow-language/cwltool#2298 · Filter by author kinow opened on Jun 28, 2026

• Allocation of CUDA devices not retrieved correctly

  common-workflow-language/cwltool#2296 · Filter by author pfennigt opened on Jun 23, 2026

• Need a better error message when using extensions without --enable-ext

  common-workflow-language/cwltool#2295 · Filter by author xdxxxdx opened on Jun 22, 2026
  3

• Resolving images with _IMAGES in SingularityCommandLineJob appears to write back to the wrong field

  common-workflow-language/cwltool#2283 · Filter by author adamnovak opened on Jun 3, 2026

• When a workflow cannot be loaded because --enable-ext was not provided, the error message does not explain this

  common-workflow-language/cwltool#2282 · Filter by author adamnovak opened on Jun 3, 2026
  1

• Use Trusted Publishing to upload to PyPI

  common-workflow-language/cwltool#2270 · Filter by author nsoranzo opened on May 21, 2026

• would make sense to support CLI argument for an input with two types: File and string

  common-workflow-language/cwltool#2251 · Filter by author volodymyrss opened on Apr 24, 2026

• --validate should check for baseCommand presence on PATH or in containers

  good first issue
  common-workflow-language/cwltool#2240 · Filter by author mr-c opened on Apr 20, 2026
  1

• Apptainer images without entrypoint not working

  common-workflow-language/cwltool#2236 · Filter by author stkgo opened on Apr 13, 2026
  2

• null wrongly requires quoting

  common-workflow-language/cwltool#2221 · Filter by author arunisaac opened on Mar 24, 2026

• loadListing behavior in workflow steps

  common-workflow-language/cwltool#2218 · Filter by author LanderOtto opened on Mar 16, 2026
  2

  

• $ escape behavior change on a second call of the same command line tool within workflow

  common-workflow-language/cwltool#2217 · Filter by author sleyn opened on Mar 11, 2026

• implement --pack using the sbpack code in cwl-utils

  good first issue
  common-workflow-language/cwltool#2212 · Filter by author mr-c opened on Mar 5, 2026

• cwltool#MPIRequirement implementation needed for Singularity

  common-workflow-language/cwltool#2208 · Filter by author kinow opened on Feb 26, 2026

• Why not using pre-commit for code linting?

  common-workflow-language/cwltool#2200 · Filter by author natthan-pigoux opened on Jan 6, 2026

• Error with conditional step and input loadContents

  common-workflow-language/cwltool#2182 · Filter by author LanderOtto opened on Nov 24, 2025

• dockerFile always built when dockerImageId specified

  common-workflow-language/cwltool#2175 · Filter by author mr-c opened on Nov 6, 2025
  1

• Schema already in use error

  common-workflow-language/cwltool#2167 · Filter by author alexiswl opened on Oct 25, 2025
  6

• cwltool fail when multiple jobs try to use the same conda env

  common-workflow-language/cwltool#2164 · Filter by author r78v10a07 opened on Oct 23, 2025
  1

• cwltool doesn't complain when max is lesser than min in ResourceRequirements

  common-workflow-language/cwltool#2163 · Filter by author Stellatsuu opened on Oct 15, 2025
  6