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Hi,
_I'll manually synchronise this issue with Jira, I've raised it here as I think it has better exposure, might be useful as a reference and I'm going to reference it from a different issue: http…
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Now that we've reconfigured and refactored the phasing pipeline to improve SV performance on 10Mbp, we probably need to make additional changes to improve scalability for whole chromosome/genome runs.…
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Currently, Optimus and SS2 pipeline tests are both run irrespectively of whether the relevant code has been updated. This ticket is for separating the tests and getting them to trigger independently d…
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Presumably on this line:
https://github.com/genome/qc-analysis-pipeline/blob/cb05da7f19972db6189b37a1ef9de6561fc0e83a/tasks/Qc.wdl#L302
I'm seeing thousands of warning messages like:
```
tar: Ig…
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A mechanism to provide a global constant that can be used in a `workflow` block, `task` block or `task command` block even if the constant isn’t made part of the task input.
Example use case is:
…
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My team would find the previously requested behaviour in dnanexus/dxWDL#168 very useful.
We are investigating switching over to WDL workflows and are almost there for one of our pipelines. However…
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Hi
I have been using WDL/Cromwell/Terra for over a year. It works great for "simple" pipeline. It has saved me a lot of time and money. I need to run something more complicated. I want to use the …
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Hi, all,
I would like to know where I can know the default parameters. Take bowtie2 as an example. I checked encode_tast_bowtie2.py and also the atac.wdl. I discovered that:
In encode_tast_bowti…
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Just realized CNV WDLs are not using NIO in FireCloud. This is as simple as changing `File` to `String` for supported files. Not sure if these need to live in our repo (I see we have a M2 NIO WDL), …
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In other words, we should validate `docker` as an optional string so that we can do things like this:
```
task foo {
String? dockerName
command { ... }
runtime {
docker: dockerName
…