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.