Updating gcp flavor of Vector pipelines to handle updates applied to farm5

malariagen / pipelines

Pipelines for processing malaria parasite and mosquito genome sequence data.

MIT License

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Closed gbggrant closed 3 years ago

gbggrant commented 3 years ago

Updating gcp flavor of Vector pipelines to handle updates applied to farm5.

Have the dockers set in the tasks, not in the runtime block
Allow alignment workflow (-> bwa) to take either read_group or read_group_id as possible parameters
Fixed bug in setting of bwa's @RG tag for when read_group_id is supplied.
Added task ExtractReadGroup, used in farm5 implementation of alignment outer pipeline.