Published September 21, 2021
| Version 3.1.20210921111717
Software
Open
common-workflow-language/cwltool: cwltool 3.1.20210921111717 ; now with podman support!
Creators
- Peter Amstutz1
- Michael R. Crusoe2
- Farah Zaib Khan3
- Stian Soiland-Reyes4
- Manvendra Singh
- Kapil kumar5
- John Chilton6
- Thomas Hickman7
- boysha
- Rupert Nash8
- Tomoya Tanjo
- ash
- Michael Kotliar9
- Brad Chapman10
- Andrey Kartashov
- Guillermo Carrasco11
- Dan Leehr12
- Nebojsa Tijanic
- Joshua C. Randall13
- Miguel Boland
- bogdang989
- Chuck McCallum
- Hervé Ménager14
- Pau Ruiz Safont15
- Denis Yuen16
- Gijs Molenaar17
- James J Porter18
- Alejandro Barrera19
- Giacomo Tagliabue20
- 1. @CuriiHQ @arvados
- 2. @common-workflow-language
- 3. The University of Melbourne
- 4. eScience lab, University of Manchester
- 5. @common-workflow-language @NITDTERRATECHNICA
- 6. Penn State University
- 7. @Genomicsplc
- 8. University of Edinburgh
- 9. Cincinnati Children's Hospital Medical Center
- 10. Ginkgo Bioworks
- 11. @iZettle
- 12. IBM
- 13. Genomics plc
- 14. Institut Pasteur
- 15. Citrix
- 16. @OICR_news
- 17. Pythonic.nl
- 18. Recurse Center
- 19. Duke University
- 20. 4Catalyzer
Description
New features:
- support (rootless) podman container engine 52e1ebe @mr-c
- Need nodejs? use podman or singularity in addition to docker bb6fe86 @mr-c
Fixes:
- CommandLineTool.arguments: correctly set $(self) 2b17b14 @mr-c
- fix add_file_or_directory_volume for singularity 7017990 @mr-c
- tweaks for testing with Singularity 3.4.x fbe4aa1 @mr-c
- cope with datetime objects 62d1e11 @mr-c
- subgraph: support long version of WorkflowStep[].out 5a1488b @mr-c
- pack: add $namespaces to the (efffective) root only (#1506) cd9fde3 @mr-c
- Fix #811 (SchemaDefRequirements not working in workflows) 8f9a9ef @ThomasHickman @mr-c
- Fix #816 (Any type in inner tool fails to run) (#1510) 23c5aab @ThomasHickman @mr-c
- schema-salad 8.2.20210914115719 fixed a bug c02bd92 @mr-c
- packing: treat the IDs of the outputs separately (#1501) 57f9be0 @mr-c
Improvements
- expression evaluation: better error messages b67a5e0 @mr-c
- (docs): grammar updates for README.rst (#1482) 952de68 @vladdoster
- more helpful message for "paths starting with '/' only permitted in CWL 1.2 and later" error @twigleingrid fed2086
Misc:
- Modernize Dockerfile; build and publish containers to quay.io a293c47 74994e5 (#1485) 1953cf6 462377e b7468c7 801a317 8ef2512 f5e5700 45be161 da64403 9fc0f2c b9fca03 f4cc3d4 @mr-c
- Update ruamel-yaml requirement from <0.17.11,>=0.15 to >=0.15,<0.17.17 abb5a7f b1bc9cf 7fe6399 05fc01b @dependabot @mr-c
- codeql: follow best practices 5356a63 330ad30 @mr-c
- allow for spaces in the current working directory 3a419f1 @mr-c
- update lingering reference to galaxy-lib 3163e89 @mr-c
- Bump codecov/codecov-action from 1 to 2.0.3 45be161 f111cf1 @dependabot @mr-c
- skip broken version of importlib_metadata 99463af @mr-c
- parallelize all tests 48c9d0c @mr-c
- cleanup requests calculations ffb7513 @mr-c
- doc: explicit mention of node.js dependency during testing (#857) 0893cbe @fgeorgatos
- add command line options to the docs 661c5d5 reduce sphinx warnings 092dd9d add docs badge c014c36 @mr-c
- add registry to dockerPull references 6a7f35f @mr-c
- fix an assert message 4ccbdde @mr-c
- mypy: warn_unreachable = True a3cc4fc @mr-c
Files
common-workflow-language/cwltool-3.1.20210921111717.zip
Files
(5.9 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/common-workflow-language/cwltool/tree/3.1.20210921111717 (URL)