Jason Cerrato
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Recent activity by Jason Cerrato
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Hi Stephanie, Thanks for writing in. Samples in a sample_set are typically interpreted as an Array[File] in a WDL. I believe it should be possible to write a task that takes the Array[File] input a...
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Hi Philipp, Apologies for the delay here! I was out sick on Friday but I will look into getting you an answer here as quickly as I can. Kind regards, Jason
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Hey Chris, I tried running this notebook in a different, older workspace and it actually seemed to work as intended. It looks like this issue crops up when using the newer style of workspace where ...
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Hey Chris, Thanks for writing in about this issue. I'm going to try and replicate this in a clone of my own. I'll get back to you as soon as I can! Kind regards, Jason
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Hey Philipp, Thanks for writing in. We'll take a closer look at this and get back to you as soon as we can. Kind regards, Jason
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Hi Aisling, If you're still interested, a member of our team will be giving that delocalization of directories idea a test try. Let us know if you would still like to see that test run happen and b...
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Hey Philipp, I'm not privy to how GATK streams files but I can try to find out next week and get back to you! For now localizing the files definitely seems like the right route. I'll follow up and ...
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To be clear, you may need to remove localization_optional for all files if samtools isn't capable of streaming in the files when given their gs:// paths.
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Hi Philipp, I see you've set localization_optional for the ref_fasta file in your WDL. I'm wondering if this is what's causing the failure with the file, because it's being told not to localize the...
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Hi Philipp, I took a look at your two submissions and noticed something interesting. In your first submission 957f51c9-c60a-4396-a2b9-bfb8ca650fe1 workflow ID 9b4c9b17-74d3-478a-b0e3-4c49faa214de I...
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