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Currently trying to use cwltool on our cluster using environment modules (@khillion and me), we have the following issue: the use of modules crashes cwltool, because it tries to store job_description …
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`cwltool --validate` accidentally accepts CWL documents in which `default` value is mismatched with the type specified in `type` field.
Is this a bug of `cwltool` or are there any descriptions in the…
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During the "Cloud Work Stream @ GA4GH 8th Plenary 2020" meeting [it was proposed](https://docs.google.com/document/u/0/d/1oAf-WF7NUPijVOhAaarDeQrAjsDFHmd7CdTOSGWuGp0/mobilebasic) that the `workflow_pa…
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Hi Kenny, I've just run the test workflow with the newest commit [681b015](https://github.com/bsmn/bsmn-common-workflow/commit/681b01549a488d4ebe05982d1742a27b80c43fad) and the run failed with the mes…
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This feature will be helpful to implement a full-featured platform with another platform that only supports CommandLineTool.
Here is a use case:
The [spec](https://www.commonwl.org/v1.2/CommandL…
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This should be added in output binding definition in spec, and conformance tests (for drafts and 1.0) which uses args.py need to have output with id args.
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# remapping
- manual annotations
# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back up and deprecate old fasta files in BLAST
- [ ] back up and deprecate old fasta files i…
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# Remapping
- manual annotations
- Monica will make sure BCM annotations are in Ag Data Commons
# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back up and deprecate old fa…
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- [x] Add `cwltool` installation instructions
- [x] Allow `cwltool` specifics to appear in example outputs. Colors, etc..
- [x] Add a `Note` about running a CWL worfklow/CLT using a generic CWL run…
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This is similar than issue #26, but I am openong a new issue in case.
We are running some tests on TESK (https://github.com/EMBL-EBI-TSI/TESK), this one fails:
```
/usr/local/bin/cwl-tes --tes…