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flagging a input Directory as writable still symlinks all files, not copy #282
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The You should be able to use a Javascript expression in the |
ok I'll try. But that seems to be quite a workaround hack to try to accomplish something quite simple? We are going to be using this quite often. Lets chat in the chat channel about extending the standard. |
I agree that a shortcut for a recursively writable input directory is
useful and a worthy addition to the spec
2017-02-02 9:30 GMT+01:00 Gijs Molenaar <notifications@github.com>:
… ok I'll try. But that seems to be quite a workaround hack to try to
accomplish something quite simple? We are going to be using this quite
often. Lets chat in the chat channel about extending the standard.
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Michael R. Crusoe
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Common Workflow Language project <http://www.commonwl.org/>
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would adding a |
My vote would be for |
A couple points:
But the spec says that when the However, But playing with this beyond-spec behavior I am not seeing a way to specify bonus: even with To summarize: We have a clear user story for marking an entire Directory tree as writable. One way forward is to issue a clarification that |
@tetron while tracing the code, I came across some strangness: https://github.com/common-workflow-language/cwltool/blob/master/cwltool/pathmapper.py#L153 |
@gijzelaerr wrong button, sorry! |
2cf0896 Merge pull request common-workflow-language#289 from denis-yuen/patch-1 68f5f90 Merge pull request common-workflow-language#291 from bmeg/master a82cf0d Merge https://github.com/bmeg/common-workflow-language e7325dc Adding docker hint for conformance test 70501d5 Merge pull request common-workflow-language#290 from alaindomissy/patch-1 58a9354 Update concepts.md 1b052b5 Fix a typo 4a02bc7 Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. 80e2501 add path to record-job3.yaml c9df19c Add checksum to cwl.output.json results. e604399 Add tests that $HOME and $TMPDIR are set correctly according to spec. a479bbd Add checksums and sizes to secondaryFiles in draft-3 tests. dfcbfeb Merge pull request common-workflow-language#286 from common-workflow-language/test-nested-array 91bb7b4 Test case for command line generation of array-of-arrays. 5baf924 Merge pull request common-workflow-language#285 from common-workflow-language/checksum-secondary 1c02570 Merge pull request common-workflow-language#282 from common-workflow-language/test-inputbinding-dir 1835540 Add checksums to secondaryFiles and files in Directory objects. 04d9dac Add test for command line inputBinding of Directory input parameter. 8053c4b Merge pull request common-workflow-language#279 from simonovic86/patch-1 168d1a2 Update README.md e727a46 Merge pull request common-workflow-language#277 from common-workflow-language/add-biostars-link bfddadc fix typo 9ec9642 add biostars link b67a4cf Merge pull request common-workflow-language#272 from StarvingMarvin/master 570ae5f Merge pull request common-workflow-language#266 from common-workflow-language/remove-empty-baseCommand 721ffdc Merge remote-tracking branch 'origin/master' into remove-empty-baseCommand 6931eeb minor userguide fixes a296c5f Remove "baseCommand: []" from tests. git-subtree-dir: cwltool/schemas git-subtree-split: 2cf0896
…ng-dir Add test for command line inputBinding of Directory input parameter.
I guess this issue can be closed? it looks working now for the new release. |
hi!
When I define an input folder as writable it is still being symlinked. Example:
But if I then look inside the intermediate cached results, the recursive directory structure is created but all files are symlinked:
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