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Support MEPRAM metadata-only downloads - #898

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albatalavera wants to merge 8 commits into
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albatalavera:develop
Closed

albatalavera wants to merge 8 commits into
BU-ISCIII:developfrom
albatalavera:develop

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@albatalavera

@albatalavera albatalavera commented Sep 10, 2026 •

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Summary

Adds support for metadata-only samples in the download module and updates the MEPRAM metadata configuration.

Changes

  • Adds --metadata-only support for download workflows.
  • Allows samples without FASTQ files to be retained in samples_data.json when metadata-only mode is enabled.
  • Uses configured MEPRAM sample ID columns instead of the old hardcoded default.
  • Skips MEPRAM template helper rows only when they are present, avoiding dropped samples after metadata merge.

PR Checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (black and flake8).
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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