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We cannot negate an exclusion pattern to exclude all folders except those that matches the pattern. Negate (!) is used within brackets [ ] as noted in the doc below - https://docs.aws.amazon.com/glue/latest/dg/define-crawler.html#crawler-data-stores-exclude
If there are too many folders, programmatically filtering and adding them in include path should help in this case.
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I don't think that's possible. What you do is multiple inputs to include each of those prd**/queries paths (maybe automating it with a small script)