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fixed some Related_To IDs in 2024_Allentoft_PostGlacial #224

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@stschiff stschiff commented Nov 29, 2024

PR Checklist for modifying one or multiple existing packages

  • The changes maintain the structural integrity of the affected packages.
  • The checksums of the modified files in the respective POSEIDON.yml files were adjusted properly.
  • Every file in the submission is correctly referenced in the relevant POSEIDON.yml files and there are no additional, supplementary files in the submission that are not documented there.

  • The packageVersion numbers of the affected packages were increased in their POSEIDON.yml files.
  • The changes in the packageVersion followed the Poseidon Package versioning policy.
  • The changes were documented in the respective CHANGELOG files. If no CHANGELOG files existed previously it was added here.
  • The lastModified fields of the affected POSEIDON.yml files were updated.
  • The contributor fields were updated with name, email and orcid of the relevant, new contributors.
  • The .janno and the .ssf files are not fully quoted, so they only use single- or double quotes ("...", '...') to enclose text fields where it is strictly necessary (i.e. their entry includes a TAB).

  • All affected packages pass a validation with trident validate --fullGeno.

  • Large genotype data files are properly tracked with Git LFS and not directly pushed to the repository. For an instruction on how to set up Git LFS please look here. If you accidentally pushed the files the wrong way you can fix it with git lfs migrate import --no-rewrite path/to/file.bed (see here).

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This PR was triggered by an observation from @Mattists that some of the samples referred to in Related_To were non-existent in the database. I found quick fixes. Perhaps good to briefly check, @smpeltola.

@stschiff stschiff self-assigned this Dec 3, 2024
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Right, I had not checked if the IDs from other publications matched those used in the Poseidon packages. Looks like your quick fixes found them all, there should be no more.

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stschiff commented Dec 3, 2024

Great, then I think this is good to merge in @AyGhal.

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