Is your feature request related to a problem? Please describe.
I am trying to create cbioportal export files, but I do not have the expression files and CNV results from snappy.
Describe the solution you'd like
We can make sub steps corresponding to CNV and transcriptomics optional and based on the config flags.
Register sub step classes so the sub steps are available
sub_classes = [
cbioportalMetaFilesStepPart,
cbioportalCaseListsStepPart,
cbioportalClinicalDataStepPart,
cbioportalMutationsStepPart,
cbioportalVcf2MafStepPart,
]
if self.config.copy_number_alteration.enabled:
sub_classes += [cbioportalCns2CnaStepPart, cbioportalCnaFilesStepPart, cbioportalSegmentStepPart]
if self.config.expression.enabled:
sub_classes += [cbioportalExpressionStepPart]
self.register_sub_step_classes(sub_classes)
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.
Is your feature request related to a problem? Please describe.
I am trying to create cbioportal export files, but I do not have the expression files and CNV results from snappy.
Describe the solution you'd like
We can make sub steps corresponding to CNV and transcriptomics optional and based on the config flags.
Register sub step classes so the sub steps are available
sub_classes = [
cbioportalMetaFilesStepPart,
cbioportalCaseListsStepPart,
cbioportalClinicalDataStepPart,
cbioportalMutationsStepPart,
cbioportalVcf2MafStepPart,
]
if self.config.copy_number_alteration.enabled:
sub_classes += [cbioportalCns2CnaStepPart, cbioportalCnaFilesStepPart, cbioportalSegmentStepPart]
if self.config.expression.enabled:
sub_classes += [cbioportalExpressionStepPart]
self.register_sub_step_classes(sub_classes)
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.