User

Sehyun Oh

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Total activity 158
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Posts

Recent activity by Sehyun Oh

  • Nested output file path

    Hi! I have an issue with output file location. Here is my workflow: https://dockstore.org/workflows/github.com/shbrief/1_mutect1_pon:master?tab=info   Output from the above workflow is saved in wor...

    • 2 followers
    • 7 comments
    • 0 votes

  • Understand ErrorReport

    Hi! I'm not sure what this error message mean. Can anyone help with it? Thanks! ErrorReport(rawls,http error calling uri https://us-central1-broad-dsde-prod.cloudfunctions.net/martha_v2,Some(502 ...

    • 6 followers
    • 23 comments
    • 0 votes

  • Task can't find localized file.

    Hi! I think my file is localized properly, but the actual run can't find/recognize it? ! I'm not sure how to resolve this. I pasted the log below. Thanks!   2020/01/28 07:28:20 Starting container s...

    • Edited
    • 2 followers
    • 13 comments
    • 0 votes

  • Data access permission issue

    Hi! I'm authorized to access TCGA controlled data, but I can't access them in Terra now. So I confirmed that, 1) my TCGA authorized NIH account is linked to Terra and not expired 2) my workspace wa...

    • 2 followers
    • 4 comments
    • 0 votes

  • 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