User

Sehyun Oh

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Recent activity by Sehyun Oh

  • Make a list of outputs

    I'm trying to build a list of output files into one file, which is used as an input for the next task. Building the output list part is keep failing. Here is my code. workflow build_normalDB {call ...

    • 2 followers
    • 5 comments
    • 0 votes

  • combine outputs

    Hi! I'm trying to combine the outputs from the previous task in my workflow, but it keeps failing. I tried scatter-gather and also tried to add an additional task (CreateFoFN, https://gatkforums.br...

    • 2 followers
    • 13 comments
    • 0 votes
    • Answered

  • input type coercion

    Hi! I'm trying to run BAM files on MuTect and SelectVariants afterwards. I provide BAM/BAI files as Array[File] to MuTect and its output is used as File input for SelectVariants. I'm getting the er...

    • Edited
    • 2 followers
    • 5 comments
    • 0 votes

  • Localization of reference files

    I'm trying to use different reference genomes (not provided in Terra's reference data), and wondering whether they need to be saved in a same folder. I was using .dict and .fai files saved in diffe...

    • 3 followers
    • 6 comments
    • 0 votes

  • Changing machine type for my tool

    I understand that 'Notebook Runtime' option on the upper right corner of workspace is only for 'Notebooks' itself, right? If so, to use a different machine for my tools, can I change the machine ty...

    • 2 followers
    • 3 comments
    • 0 votes

  • Data entity type for MuTect

    Hi! I'm quite confused about which data entity I should use for my workflow. I'm trying to run MuTect_v1 on both tumor/normal paired-mode for SNV detection and on artifact-detection-mode for PoN co...

    • Edited
    • 2 followers
    • 11 comments
    • 0 votes

  • Environmental variable for notebook

    Hi! I followed this post (https://broadinstitute.zendesk.com/hc/en-us/articles/360026639112-New-Environmental-Variables-for-Jupyter-Notebooks), but found out neither $WORKSPACE_NAME nor $WORKSPACE_...

    • 3 followers
    • 11 comments
    • 0 votes

  • Data transfer between Notebook and the rest of the workspace

    Hi! I'm trying to use notebook and data/tools in workspace interactively and having some issues. I uploaded my file through Terra (Data > Other Data > Files > notebook (directory) > + (upload butto...

    • 2 followers
    • 3 comments
    • 1 vote

  • Efficient way to 'Select samples to process' in Terra?

    Hi! I really like that Terra offers a function to select specific samples to process - if this was in FireCloud, I couldn't find it at least, I guess. I'm wondering whether there is any efficient w...

    • 3 followers
    • 7 comments
    • 0 votes

  • Format of the custom table for the flexible data model

    I want to use custom tables for data models and wonder what is the format of tsv file. For example, when I uploaded the manifest file from GDC, I got this error: File does not start with entity or ...

    • 3 followers
    • 7 comments
    • 0 votes