The modern WDL spec has clarified that the end user can never override assignments to task inputs made in workflow code. This means that classify_single's two invocations of the metagenomics.filter_bam_to_taxa task (with different default input values for each call) has inputs that are not user-editable as we intended. The only workaround appears to be to promote these task inputs to boilerplate workflow inputs that have default values (and are overridable by the end user).
The modern WDL spec has clarified that the end user can never override assignments to task inputs made in workflow code. This means that
classify_single's two invocations of themetagenomics.filter_bam_to_taxatask (with different default input values for each call) has inputs that are not user-editable as we intended. The only workaround appears to be to promote these task inputs to boilerplate workflow inputs that have default values (and are overridable by the end user).