
Ash O'Farrell
Activity overview
Latest activity by Ash O'Farrell
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Ash O'Farrell commented,
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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Ash O'Farrell commented,
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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Ash O'Farrell commented,
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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Ash O'Farrell commented,
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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Ash O'Farrell commented,
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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Ash O'Farrell commented,
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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Ash O'Farrell commented,
Did permissions change relatively recently? Previously, I was able to view costs after workflows run on billing projects on which I'm not the owner. Now I see N/A for everything (after waiting for ...
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Ash O'Farrell commented,
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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Ash O'Farrell commented,
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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Ash O'Farrell commented,
I'm definitely interested, thanks for keeping me in the loop as this develops!
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