User

Stephanie Gogarten

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Activity overview

Latest activity by Stephanie Gogarten

  • Stephanie Gogarten created a post,

    Workflow outputs not displayed in Job History "outputs" tab

    In the main Job History page on Terra, the "Outputs" tab only contains values if the workflow was run on a data table. If the workflow was run on file paths so that outputs are not written to a dat...

    • Stephanie Gogarten
    • Edited
    • 2 followers
    • 1 comment
    • 0 votes
  • Stephanie Gogarten created a post,

    Copy RStudio html output to notebooks/

    When syncing an RStudio notebook to the notebooks/ folder, it would be very helpful to copy the .nb.html file as well as the .Rmd file. This way users would be able to view the output of their note...

    • Stephanie Gogarten
    • 2 followers
    • 1 comment
    • 0 votes
  • Stephanie Gogarten commented,

    I submitted a separate ticket about the error in relinking accounts; it was a bug and has now been fixed. The issue above seems to have resolved as well; `tnu drs info` gives the expected response.

  • Stephanie Gogarten created a post,

    tnu drs commands returning error code

    I'm trying to use a controlled-access file with a drs link in the terminal from an RStudio cloud environment on Terra. I can copy the curl command to download the file via the File browser and run ...

    • Stephanie Gogarten
    • 2 followers
    • 2 comments
    • 0 votes
  • Stephanie Gogarten commented,

    Thanks Ash! I feel like the bigger issue here is a failure of Dockstore search, because even knowing that the exact workflow I want exists, it's not straightforward to find it. I posted about this ...

  • Stephanie Gogarten commented,

    Is there now a readily available WDL to run `samtools index`? I tried searching for one on dockstore, but got >200 results for WDLs that contain indexing somewhere as a step. I also tried searching...

  • Stephanie Gogarten created a post,

    Workflow succeeded despite error code

    I am writing a workflow that contains a series of commands in the command block. If the final command returns an error code, the workflow fails, but if an earlier command in the series returns an e...

    • Stephanie Gogarten
    • Edited
    • 2 followers
    • 1 comment
    • 0 votes
  • Stephanie Gogarten created a post,

    Size limits on data tables?

    We are trying to create very large data tables in a workspace to track simulated genotype data. We are using the Bioconductor::AnVIL R functions avtable_import and avtable_import_set to write to th...

    • Stephanie Gogarten
    • 2 followers
    • 1 comment
    • 0 votes
  • Stephanie Gogarten created a post,

    Latest 1000G VCF files on AnVIL?

    Are the most recent VCF files from the high-coverage 1000 Genomes dataset available on AnVIL, or are there plans to make them available soon? The 1000 Genomes public workspace only has the much old...

    • Stephanie Gogarten
    • 2 followers
    • 1 comment
    • 0 votes
  • Stephanie Gogarten commented,

    Is it possible to preserve the ordering in the initial TSV file (or Python/R table when interacting with data tables programmatically)? Our project will be creating hundreds of workspaces, so chang...