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IDAT entry_point. #359

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IDAT entry_point. #359

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rajwanir
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This PR adds IDAT entry_point and makes the workflow truly raw data to QC report.

  1. The IDAT entry point uses a Illumina's free Dragena software (https://help.dragenarray.illumina.com/product-guides/dragen-array-local-analysis) for converting IDAT to GTC (383b89b). Since Dragena is Illumina's proprietary software and unavailable via Conda, the pipliene can only use it as an enviornment module.
  2. Non-CCAD2 users can download the dragen array from Illumina's website and provide a path to dragena binary via the dragena_location option in config to use the IDAT entry_point (see 55655f6).
  3. After IDAT to GTC conversion, the workflow resumes GTC entry point with either BCF or PED option. (13cf63d)
  4. The IDAT entry point can run both locally and in cluster_mode (13cf63d)

I can update the docs once PR is finalized. Thank you.

@rajwanir rajwanir requested a review from jaamarks November 25, 2024 20:21
@rajwanir rajwanir self-assigned this Nov 25, 2024
@rajwanir rajwanir added the enhancement New feature or request label Nov 25, 2024
@jaamarks
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Concept ACK - will test.

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