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As far as I remember, in the Past it was possible to reference global workflow variables inside a task. But now I get wdl validation errors like this:
```
ERROR: Variable genome does not reference a…
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When a WDL task fails (run via AGC), I've observed that all other tasks are killed. I'd like `miniwdl` to execute as many tasks as possible until there are no more tasks that are independent of the f…
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The current wdl files were developed with DNANexus in mind. I am trying to modify and use in Cromwell, and it seems there are differences in the way paths for sub-workflows are handled vs. DNANexus. I…
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WDL tasks localize during JES runs using WDL like so:
```
task myTask {
File myFileToLocalize
Array[File] otherFilesToLocalize
...
command >
...
```
also, WDL tasks can specif…
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In the spec it appears that inputs are only allowed to be of the form:
```
{
"url": "s3://my-object-store/file1",
"path": "/data/file1"
}
```
Implying inputs must only be files.
…
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Hi folks,
Would it be possible to support optional linting against a "style guide"?
We could describe conventions for workflow/task/variable/.. names (e.g. as regexes), newlines/tabs/spaces with…
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From WDL [spec](https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#string-substring-string-string):
>this function replaces all non-overlapping occurrences of pattern in input by…
kinow updated
2 years ago
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I'm trying to help @jrotieno debug the mpxv workflow but I don't know how to run a workflow locally.
The README currently states:
>These workflows are written in [WDL](https://github.com/openwdl/w…
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I'm not 100% sure this is an issue with the syntax highlighter, but if in Sublime Text I use `CTRL+/` (or select the equivalent from the menu), it does not toggle the comment status of the current lin…
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:cool:
### :pushpin: Explain the Request
Some GenBank accessions are unable to be downloaded via the command we currently have in the Assembly_fetch workflow:
```
datasets download genome ac…