Rename data_type to seq_data_type

GargGroup / BioDivGenomics

MIT License

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Rename data_type to seq_data_type #37

Open junaruga opened 1 year ago

junaruga commented 1 year ago

This issue ticket is for a task note. Rename the current input parameter data_type ("HIFI"/"ONT") to seq_data_type. Because we want to add a new input parameter genome_data_type.

seq_data_type: "HIFI" or "ONT"
genome_data_type: ("organelle" or "mitochondria") or "" (empty). Note the mitochondria is a part of the organelle.

junaruga commented 1 year ago

Note the optional parameters for the contamination in the "human-pangenomics/hpp_production_workflows" are below. It's not "organelle" but "mitochondria".

Eukaryotic
Mitochondria
Plastids
Vecscreen
RRNA

https://github.com/human-pangenomics/hpp_production_workflows/blob/3085f434d706dd416920dc3833ea296e886045cf/QC/wdl/tasks/contamination.wdl#L7-L14