User

Alex O

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Recent activity by Alex O

  • Outputting and inputting a directory

    I'm writing a wdl that uses both salmon index and salmon quant. It runs fine locally using:task index {...output {    File salmonindex }...}=>input {    File index.salmonindex}But running on ter...

    • 2 followers
    • 6 comments
    • 0 votes

  • Cannot look up input variable, variable never declared

    I'm trying to import an established, but modified workflow into a new workflow I'm writing, but I keep getting this error when trying to generate inputs:   Failed to process workflow definition 'an...

    • Edited
    • 3 followers
    • 14 comments
    • 0 votes

  • Referring to folders in WDL

    I'm writing a wdl file for a series of tools, one of which is hisat2. hisat2 requires a folder of hisat-index data, and uses all of the files in that folder. How do I reference this in the wdl file...

    • 4 followers
    • 5 comments
    • 0 votes

  • Download from SRA tool inputs

    The workflow DownloadFromSRA (long-read-pipelines/DownloadFromSRA/2) requests a column for the SRA ID and a gcs_output_dir. Does this tool require me to use a preexisting GCS bucket? I tried using ...

    • Edited
    • 2 followers
    • 13 comments
    • 0 votes

  • Calling tools in wdl

    How would I make a tool that is normally called from a binary available to workflow? As an example, the fastqc workflow simply calls fastqc, but I don't know how it makes the command available to b...

    • 2 followers
    • 9 comments
    • 0 votes

  • The WDL tutorial 1 does not work

    The current wdl tutorial files and instructions are not current with the programs or filenames that are being used, causing the tutorial to no longer function as published. For more information as ...

    • Edited
    • 2 followers
    • 2 comments
    • 0 votes
    • Completed