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Is there an updated MutationCalling_Mutect_v1-2_BETA_cfg?

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

java -jar $wdltool graph --all MutationCalling_Mutect_v1-2_BETA_cfg.txt > mutationcalling_mutect_v1-2_BETA_cfg.dot
Exception in thread "main" wdl4s.parser.WdlParser$SyntaxError: ERROR: Expression references output on call that doesn't exist (line 594, col 9):

           VEP_Task.VEP_VCF
        ^

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.


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