User

Ash O'Farrell

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Total activity 97
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Posts

Recent activity by Ash O'Farrell

  • How do I pass an array(array(file)) to another task?

    I have a task that takes in a bunch of RData files, matches them according to the chr number they are associated with, and should export them as an Array[Array[File]]. Something similar is done in ...

    • Edited
    • 3 followers
    • 13 comments
    • 0 votes

  • Docker Hub login error on scattered task

    I have a workflow with a scattered task that scatters to approximately 50 instances. It appears that in three of those instances, the images failed to pull from Docker Hub. They are all using the s...

    • 2 followers
    • 4 comments
    • 0 votes

  • select_first() doesn't function as expected on optional outputs

    I've been struggling to get a workflow to work in Terra. In attempts to narrow down the issue I've ended up with a workflow that looks completely arbitrary, but I promise I came across this issue i...

    • Edited
    • 4 followers
    • 14 comments
    • 0 votes
    • Answered

  • basename() does not function as expected on DRS URIs

    There seems to be a bug with the WDL function basename() when it is run on files that originate via DRS URIs. Instead of giving the basename, it is pulling the name of the folder is being localized...

    • 5 followers
    • 9 comments
    • 0 votes
    • Answered

  • Is it possible to have a task directly modify an input file?

    While working on converting UWGAC workflows from CWL into WDL as part of BioData Catalyst, I came across one that caused a permissions issue. For weeks I thought this was due to the fact I was usin...

    • 3 followers
    • 19 comments
    • 0 votes

  • Cannot update workflow if current snapshot active on Terra becomes invalid

    In summary: If a syntax error occurs in a workflow that is already in a workspace, that workflow cannot be updated nor used in that workspace anymore. Usually syntax errors would be detected before...

    • 2 followers
    • 3 comments
    • 0 votes

  • Terra seems to have destroyed my output

    I am developing this WDL on Terra for a BioData Catalyst fellow. It works fine when run locally, but when run on Terra the final output is destroyed. Call cacheing disabled, delete intermediates di...

    • Edited
    • 2 followers
    • 12 comments
    • 0 votes

  • Paused environment sometimes doesn't spin back up

    I had the following cloud environment paused: Hail, no startup script Master: 8 CPUs, 30 mem, 500 GB Workers: 2 workers, 120 preempts, 8 CPUs, 30 mem, 100 GB I deleted the notebook I started the ...

    • 2 followers
    • 1 comment
    • 0 votes

  • Terra sometimes misreports workflow times

    I ran the TOPMed Aligner WDL on 10 controlled-access CRAMs to benchmark costs as part of BioData Catalysts W3.1's benchmarking goal. I noticed the time that some steps took to complete seemed off, ...

    • Edited
    • 3 followers
    • 7 comments
    • 0 votes
    • Answered

  • Cannot delete Terra workspace due to apparent MySQL error

    I am attempting to delete a workspace that contains controlled access TOPMed data (hence me not adding support to the workspace) that is costing about 80 cents a months in storage costs. Unfortunat...

    • 2 followers
    • 11 comments
    • 0 votes