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Undeclared parameter exception is not case sensitive when scanning steps. #290

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mmterpstra opened this issue Apr 21, 2022 · 0 comments

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@mmterpstra
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Undeclared parameter exception is not case sensitive when scanning steps.
my error:

Exception in thread "main" java.lang.Exception: Parameter 'pipelineutilMod' used in steps [Lofreq, Mutect2Pon, MergeMutect2PonVariantsByProject, Mutect2, Lancet, Freebayes, MergeMutect2VariantsByProject, CombineVariants, VariantAnnotation, CustTumorNormalAnnotations, IndelVariantsToTable, IndelVariantsToMinTable, SNVVariantsToTable, SNVVariantsToMinTable, IndelVariantsToDescriptionTable, SNVVariantsToDescriptionTable, TablesToSplitTables, PlotGenome, MergeSegFiles] does not have a value in any of the parameter files

what it should output

Exception in thread "main" java.lang.Exception: Parameter 'pipelineutilMod' used in steps [Lofreq] does not have a value in any of the parameter files

ez replication:

create #string INPUT in the step 2 in this example:
https://rawgit.com/molgenis/molgenis-compute/master/molgenis-compute-core/README.html

this will produce something like

Exception in thread "main" java.lang.Exception: Parameter 'INPUT' used in steps [step_1,step_2] does not have a value in any of the parameter files
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