Is there a way to control the processing order so that the first part of processing, which creates a backup file, completes before the second part of processing starts. I don't want the second part to start processing on the file before the backup of that file can be created.
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To make sure that a workspace writes a backup before starting the second part of processing you could use a FeatureWriter to write the backup. This transformer would return a summary feature once the backup is written, which could then trigger either the next transformer or a reader for the second part of processing with the FeatureReader.
These articles are a great introduction to the FeatureReader & FeatureWriter transformers:
https://knowledge.safe.com/articles/24082/basic-featurewriter-example.html
https://knowledge.safe.com/articles/23538/the-featurereader-transformer.html