Ash O'Farrell

1. Terra on Google Cloud
2. ...
3. Workflow errors and issues
4. Issue: Slow localization of input files

It turns out this also helps with slow delocalization of files at the end of a task too! Throwing more space (and an SSD) at a task slashed the delocalization time of its outputs by almost 75%. Tha...

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• June 16, 2022 23:08
• 1 vote

1. Terra on Google Cloud
2. ...
3. Frequently Asked WDLs Questions
4. Can runtime parameter values be generated dynamically?

This does not appear to work in WDL 1.0, but there is still a way to do this! You can actually declare variables outside of the input or command sections, and those variables can be functions of va...

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• Edited February 25, 2022 21:39
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1. Community
2. General Discussion
3. How do I pass an array(array(file)) to another task?

I'm wondering if it might be a good idea to use this as opportunity for a wider discussion. Based on my own experience and from talking with a few BDC fellows, I have found that there is some probl...

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• November 17, 2021 21:28
• 1 vote

1. Terra on Google Cloud
2. ...
3. Workflows setup
4. How to configure workflow inputs

The textbox at the bottom referencing "T101 Workflows QuickStart (click for guide)"  to address https://support.terra.bio/hc/en-us/articles/9612163744923 is a 404. Any users reading this, you might...

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• May 05, 2026 19:55
• 0 votes

1. Community
2. General Discussion
3. How to index a CRAM file on Terra with samtools?

Hello Stephanie! Originally this question was about Jupyter instead of WDL, but I think I can help out here. I just whipped up a simple samtools index WDL workflow for you and put it on Dockstore. ...

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• Edited August 30, 2023 19:33
• 0 votes

1. Community
2. Known Issues
3. select_first() doesn't function as expected on optional outputs

I essentially want to coerce Array[Array[File]?] created via a scattered task's glob() into Array[Array[File]], because trying to scatter on arrays with optional types is a headache and/or not poss...

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• Edited February 02, 2023 22:17
• 0 votes

1. Community
2. Known Issues
3. select_first() doesn't function as expected on optional outputs

This isn't urgent, feel free to address this when you can. So I put together a flowchart explaining how the workflow works: https://github.com/aofarrel/myco/blob/main/doc/overview.md Note that the ...

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• December 21, 2022 21:54
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1. Community
2. Known Issues
3. select_first() doesn't function as expected on optional outputs

Yes, this is relevant to the other thread too. I again had select_all() not working as expected, this time on file outputs. I wrote a thread about it on the OpenWDL Slack, which I'll summarize here...

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• December 20, 2022 20:16
• 0 votes

1. Community
2. Known Issues
3. select_first() doesn't function as expected on optional outputs

I've recently started seeing some odd behavior with select_all() as well, where null outputs appear to not be getting dropped. I'm wondering if that might be related to this bug. Has there been an ...

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• December 16, 2022 22:46
• 0 votes

1. Community
2. Completed Feature Requests
3. Switch Localization/Delocalization From gsutil to gcloud storage

Chiming in to agree. Right now, localization and delocalization is pretty slow. Even after doing what's suggested here plus switching to SSDs, I'm seeing speeds of about 150 GB/hour. For comparison...

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• November 30, 2022 22:14
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