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womtool validation error using new mitochondrial pipeline

jipvdinterjipvdinter NetherlandsMember
Hi,

I am currently modifying the M2 mitochondrial workflow WDLs to make them compatible with our local HPC. When I try to validate them using womtools v47, the program clears my version of AlignmentPipeline.wdl. However, the other two WDLs throw an error:

Failed to import AlignmentPipeline_myedit.wdl (reason 1 of 1): Failed to read task definition at line 71 column 6 (reason 1 of 1): Cannot mix leading whitespace characters in command ["\n", " "].

command used in windows CMD:

java -jar C:\path\womtool-47.jar validate D:\path\AlignAndCall_myedit.wdl

When I tried it with the original GATK WDL directly downloaded from github, it returns roughly the same error; failure to import due to mix of whitespace characters. Is that intended or might this be a bug in the womtools software?

Failed to import AlignmentPipeline.wdl (reason 1 of 2): Failed to read task definition at line 56 column 6 (reason 1 of 1): Cannot mix leading whitespace characters in command ["\n", " "].
Failed to import AlignmentPipeline.wdl (reason 1 of 2): Failed to read task definition at line 165 column 6 (reason 1 of 1): Cannot mix leading whitespace characters in command ["\n", " "].

kind regards,

Jip

WDL files:
https://github.com/broadinstitute/gatk/tree/master/scripts/mitochondria_m2_wdl

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