diff --git a/pipeline_utils/lib/yaml_parser.py b/pipeline_utils/lib/yaml_parser.py index 4149d80..12bc075 100644 --- a/pipeline_utils/lib/yaml_parser.py +++ b/pipeline_utils/lib/yaml_parser.py @@ -339,6 +339,8 @@ class YAMLMetaWorkflow(YAMLTemplate): RULE_SCHEMA = 'rule' FLAG_SCHEMA = 'flag' QC_RULE_SCHEMA = 'qc_rule' + QC_RULESET_SCHEMA = 'qc_ruleset' + QC_RULESET_PORTAL_SCHEMA = 'QC ruleset' def __init__(self, data): """Constructor method. @@ -362,6 +364,9 @@ def _arguments(self, input, consortia): self.ARGUMENT_NAME_SCHEMA: name, self.ARGUMENT_TYPE_SCHEMA: type } + if type == self.QC_RULESET_SCHEMA: # replacing qc_ruleset + # with portal correspoding key + argument_[self.ARGUMENT_TYPE_SCHEMA] = self.QC_RULESET_PORTAL_SCHEMA if type == self.PARAMETER_SCHEMA: argument_[self.VALUE_TYPE_SCHEMA] = format for k, v in values.items(): diff --git a/pipeline_utils/schemas/yaml_metaworkflow.py b/pipeline_utils/schemas/yaml_metaworkflow.py index 743e1b2..84a0dad 100644 --- a/pipeline_utils/schemas/yaml_metaworkflow.py +++ b/pipeline_utils/schemas/yaml_metaworkflow.py @@ -94,7 +94,7 @@ schema.PROPERTIES: { 'argument_type': { schema.TYPE: schema.STRING, - schema.PATTERN: '^file\\..+|^parameter\\..+' + schema.PATTERN: '^file\\..+|^parameter\\..+|^qc_ruleset\\..+' }, 'dimensionality': { schema.TYPE: schema.NUMBER