Ash O'Farrell

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2. General Discussion
3. How do I pass an array(array(file)) to another task?

Hey Jason, Sorry about my slow response, I have been OOO. I'm definitely interested in the delocalization of directories idea. Not sure if it would work for my use case, but it's worth a shot. I'm ...

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• November 15, 2021 18:25
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1. Community
2. General Discussion
3. How do I pass an array(array(file)) to another task?

Workspace link: https://terra.biodatacatalyst.nhlbi.nih.gov/#workspaces/anvil-stage-demo/assoc%20PUBLIC/, it's only got public data Submission IDs (each have only one workflow ID): 64546485-bec7...

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• Edited November 03, 2021 16:19
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3. Docker Hub login error on scattered task

I haven't been able to replicate the error, no. Perhaps it was a temporary limit?

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• October 21, 2021 15:56
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3. Is it possible to have a task directly modify an input file?

I have already re-written the task in question to avoid this by simply duplicating the input and running the Rscript on the duplicate, but my new WDL (exact same Docker image so permissions still a...

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• September 17, 2021 20:20
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3. Is it possible to have a task directly modify an input file?

The R script I am running is using openfn to open a gds file. Normally this function opens in read-only mode, but the R script specifically disables this, thereby attempting to open the file in a w...

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• September 01, 2021 19:40
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1. Community
2. General Discussion
3. Is it possible to have a task directly modify an input file?

Am I understanding the suggestion correctly? Is it this? sudo su - rootRscript /usr/local/analysis_pipeline/R/unique_variant_ids.R unique_variant_ids.config This results in this appearing in the lo...

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• September 01, 2021 01:41
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2. Known Issues
3. select_first() doesn't function as expected on optional outputs

I'm so used to working with controlled data I didn't even think of that. It's all public data this time, support has been added. Workspace link: https://terra.biodatacatalyst.nhlbi.nih.gov/#workspa...

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• August 26, 2021 16:40
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2. Known Issues
3. basename() does not function as expected on DRS URIs

Thanks for always being quick to respond Jason! It's much appreciated!

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• August 19, 2021 16:07
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2. General Discussion
3. Is it possible to have a task directly modify an input file?

I might be barking up the wrong tree here, but it seems that when Terra localizes files, those files are considered owned by root instead of the topmed user (which is considered the owner on local ...

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• August 11, 2021 21:30
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1. Community
2. General Discussion
3. Is it possible to have a task directly modify an input file?

Interestingly, when I run this modified workflow on Terra, whoami still resolves to the topmed user, and the topmed user still is in the sudo group. Who am I? topmed What's in the group database? r...

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• August 11, 2021 21:10
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