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You could control it that way:

meta:
  extract_upstream: false

tasks:
  - source: scripts/get.py
    product: out/get.ipynb

  - source: scripts/second.py
    product: out/second.ipynb
    upstream: [get]

  - source: scripts/third.py
    product: out/third.ipynb
    upstream: [second]

The

extract_upstream: false

turn off the automatic extraction from the script.