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I am trying to run a workflow with a subworkflow that has some workflow level inputs. Somethign along the lines of
```
Workflow subWorkflow {
File f
String s
...
...
}
```
```
import "…
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# Independent user test of GATK-SV single-sample pipeline on Biowulf
Ben previously configured the GATK-SV single-sample pipeline for Biowulf and tested using a COVNET WGS sample. I ran an independ…
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This issue was prompted by the following thread on the forum: https://gatkforums.broadinstitute.org/wdl/discussion/10347/localization-via-hard-link-has-failed
By default, cromwell does not specify …
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Dear all,
I am trying to run your ATAC pipeline, launching the following script with qsub on our cluster:
************************ lc.sh ************************
source /abcd/conda.sh
conda …
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Since `PostprocessGermlineCNVCalls` processes individual samples, it makes sense to reorganize gCNV calls into separate tarballs for each sample in the _COHORT_ WDL (v.s. one tarball containing calls …
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In our current invocations in the WDL workflow, we run kraken, and then krona, on a bunch of samples to save on DB staging time and such. Currently, the krona portion is run in a for-loop after kraken…
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**Describe the bug - Dockstore mismatch**
When a .dockstore.yml workflow is updated via a typical push from GitHub, what appears on dockstore.org can be updated faster than what appears if you try to …
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While running `gradlew setupDecompWorkspace build` (After building begradle), I get the following error:
--------------------------------------------------------------------------------------------…
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In practice, some outputs of a workflow may be very voluminous but of low value to persist beyond immediate execution, and it would be useful to be able to tag such cases, say, with a hint for workflo…
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**_Are you seeing something that looks like a bug? Please attach as much information as possible._**
No. The job is killed because of memory limitations _e.g_ `/bin/bash: line 1: 172 Killed`
…