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common-workflow-language / cwltool

Common Workflow Language reference implementation
https://cwltool.readthedocs.io/
Apache License 2.0
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regression: --pack, relative run references when loading from a URL #1077

Open mr-c opened 5 years ago

mr-c commented 5 years ago

works in cwltool version 1.0.20181217162649 but not version 1.0.20190228155703

$ cwltool --pack https://raw.githubusercontent.com/NCI-GDC/gdc-dnaseq-cwl/3cb464a3a5c39cc060cd23d9c60918bc9ffb169b/workflows/bamfastq_align/etl.cwl
/home/michael/cwltool/tempenv3/bin/cwltool 1.0.20190228155703
Tool definition failed initialization:
[Errno 2] No such file or directory: '/home/tools/bio_client_download.cwl'

(but cwltool --validate does work)

526f36f93655bfb098f766ff020708b5a707513a is the first bad commit

according to git bisect

mr-c commented 5 years ago

Using the previous commit with the newer schema_salad is not sufficient to cause --pack to fail in this circumstance.