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Is there an updated MutationCalling_Mutect_v1-2_BETA_cfg?

shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

I'm asking because the CallingGroup_Workflow within the MutationCalling_Mutect_v1-2_BETA_cfg produces a wdltool error:

java -jar $wdltool graph --all MutationCalling_Mutect_v1-2_BETA_cfg.txt >
Exception in thread "main" wdl4s.parser.WdlParser$SyntaxError: ERROR: Expression references output on call that doesn't exist (line 594, col 9):


I also noticed that although the variant_effect_output.txt file is full of annotated records, the vepReport.html from Variant classes onwards is blank.

Here's where I think is the problem. The VEP_Task (truncated below) does not produce an output VEP_VCF. Rather, it produces outputs called VEP_Output and VEP_Report.

task VEP_Task {
    output {
        File VEP_Output="variant_effect_output.txt"
        File VEP_Report="variant_effect_output.txt_summary.html"

So I'm wondering if an updated CFG is available. Thanks.

Best Answer


  • esalinasesalinas BroadMember, Broadie ✭✭✭

    I'm pretty sure you have the latest version of the WDL with v1-2_BETA_cfg

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Yes, opening the downloaded HTML file allows me to view the contents of the report. Thanks for the tip!

    I'm using the latest wdltool (wdltool-0.8.jar) locally. Wdltool accepts a modified script that deletes the line that gives the error.

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    At the time of wdl-writing the latest version of wdl-tool was either 0.4 or 0.5.....

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    @shlee I believe there is a documentation somewhere that says to download the HTML file.
    also, I think the reason it's blank is due to a javascript security setting/issue

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