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If output of task A is read by task B, and both tasks support streaming, then they can be run in parallel, rather than sequentially, using a named pipe to stream A's output to B's input (or a socket …
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**Blocked by WDL features**
**Why?** Previously both WDL and the HCA data store were unable to support directory structures by having
```java
/
```
in filenames. We use zarr as one of our sparse m…
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Something seemed to have changed around Singularity v4 that prevents Singularity from pulling images that are too old:
```
$ singularity --version
singularity-ce version 4.0.3-jammy
$ singularity …
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I see the `.dockstore.yml`. What is the URL on https://dockstore.org/ for this repository? I am interested in seeing the page. Thanks.
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Agree upon, and document conventions:
* consistent scheme for controlling vg docker image version throughout workflows
* tasks/workflows factorization, and import directories
* camel-casing vs un…
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I want to set AWS_BATCH_JOB_ATTEMPT in my pipeline. My pipeline is a cromwell wdl pipeline which utilizes AWS batch as the backend. I submit jobs like so
```
curl -X PO…
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Not consistent with best practices and will be a maintenance headache.
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**Problem:**
Cromwell's GCP backend supports optional localization of files, via the "parameter_meta" section, such as in this example:
https://github.com/broadinstitute/warp/blob/2b0493125cae26b71f…
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Hi!
I ran the standard_haploid_qc workflow and saw that it was using a really old version of minimap2 in the asmgene call.
The asmgene task (here: https://github.com/human-pangenomics/hpp_produ…
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As with cwlpack, it looks like WDL has some utilities to gather imports at a particular time. This is required for reproducibility.
There might be code that can be re-used in WARP
> "Because we have …