User

Stephen Fleming

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Recent activity by Stephen Fleming

  • Specify Array[File] output for a task in a WDL

    I had a question about how to specify a `task` output that is an array of files `Array[File]`.  Chris Llanwarne answered my question, and so I will post it here.   Short version: ------------------...

    • 3 followers
    • 1 comment
    • 0 votes

  • Long-running command in Terra Cloud Environment terminal

    I have a long-running command I'd like to run in the terminal on a Terra workspace Cloud Environment.  I'd like it to be able to crank away on a GPU for days, in some cases. There seems to be a tim...

    • 3 followers
    • 3 comments
    • 1 vote

  • Workflow auto-retry based on error message

    Could we get the ability to automatically retry a failed workflow for certain specific failure messages in Terra?  For example, if I see the string "Execution failed: generic::unknown: installing d...

    • 2 followers
    • 2 comments
    • 1 vote

  • WDL versions supported by Terra

    Which versions of WDL are we able to use in workflows in Terra? I've used "draft-2" and "1.0" in the past.  But there is a feature in WDL 1.1 that I want to use.  Can we use WDL version 1.1 in Terra?

    • 3 followers
    • 5 comments
    • 1 vote

  • Support folders (in addition to files) in the Terra data table

    Currently, when I click on an entry in the Terra data table that points to a folder (by which I mean a google bucket path that is not a concrete file), I see something like this Technically the me...

    • 3 followers
    • 3 comments
    • 7 votes

  • Alternative to archiving workflow metadata

    I've now been running WDLs in Terra long enough that some older workflow details have been archived.  In my experience, it is very common to need to go back past a year to look for details of old w...

    • 2 followers
    • 1 comment
    • 1 vote

  • The "where did this file come from?" feature

    Can Terra implement a "where did this file come from?" feature?The idea would be that you can point to a file in the Terra data table, and (if it was generated by a workflow) it will tell you which...

    • 3 followers
    • 3 comments
    • 9 votes
    • Completed

  • Scatter: over chunks rather than for each

    Hello! I have a specific question about scattering in a WDL.  What I want to do is a lot like this scatter (file in file_array) { call task{input: file=file}} except that, in my case, it is horrib...

    • 2 followers
    • 4 comments
    • 0 votes

  • Cromwell execution directory

    Cromwell question: is there an environment variable that I can access from within a running task's command block that specifies the Cromwell execution directory (google bucket) ?

    • 2 followers
    • 4 comments
    • 1 vote

  • Possible to clone a notebook VM?

    Hello! I want to enable somebody else on my billing project to work in the exact same notebook environment I am working in. I realize that the real goal is to have a nice docker image so that you c...

    • 2 followers
    • 4 comments
    • 0 votes