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**Is your feature request related to a problem? Please describe.**
https://github.com/DataBiosphere/analysis_pipeline_WDL has multiple workflows which are beautifully handled by a .dockstore.yml (seri…
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Right now, `Job` ~has both a `chainedJobs` field, which is a list of `str()` on each job in the chain in order, used by the stats and logging system to dump the worker's log to per-job files, and also…
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For example in `CombineGVCFs.wdl` one can see indexOutput as optional input argument:
```
# Required Arguments
String output_arg
String? outputIndex
```
(first of all, outputIndex is …
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This issue ticket is for a task note. Rename the current input parameter `data_type` ("HIFI"/"ONT") to `seq_data_type`. Because we want to add a new input parameter `genome_data_type`.
* `seq_data_…
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**Is your feature request related to a problem? Please describe.**
Perhaps this is intended, in which case this ticket can be rejected, but I found the way the UI surfaces the TRS URL and TRS ID (main…
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**Is your feature request related to a problem? Please describe.**
Workflows with HTTP imports are not very reproducible. It should be discouraged.
**Describe the solution you'd like**
Add to the bes…
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In several immuno.wdl runs we have encountered errors during the localization step.
These errors look something like this:
```
Sep 02 11:31:08 malachi-immuno-5120-34 java[12774]: 2024-09-02 11:…
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Hello
I have encountered the following problem:
I have a workflow that contains (among others) the two tasks GetBwaVersion and MergeBamAlignment.
MergeBamAlignment takes as an input the outpu…
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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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WDL tasks localize during JES runs using WDL like so:
```
task myTask {
File myFileToLocalize
Array[File] otherFilesToLocalize
...
command >
...
```
also, WDL tasks can specif…