2023_Rivollat_ExtensivePedigrees

[93Boy]

PR Checklist for a new package submission

• The package does not exist already in the community archive, also not with a different name.
• The package title in the POSEIDON.yml conforms to the general title structure suggested here: <Year>_<Last name of first author>_<Region, time period or special feature of the paper>, e.g. 2021_Zegarac_SoutheasternEurope, 2021_SeguinOrlando_BellBeaker or 2021_Kivisild_MedievalEstonia.
• The package is stored in a directory that is named like the package title.

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• The package is complete and features the following elements:
  • Genotype data in binary PLINK format (not EIGENSTRAT format).
  • A POSEIDON.yml file with not just the file-referencing fields, but also the following meta-information fields present and filled: poseidonVersion, title, description, contributor, packageVersion, lastModified (see here for their definition)
  • A reasonably filled .janno file (for a list of available fields look here and here for more detailed documentation about them).
  • A .bib file with the necessary literature references for each sample in the .janno file.
• Every file in the submission is correctly referenced in the POSEIDON.yml file and there are no additional, supplementary files in the submission that are not documented there.
• Genotype data, .janno and .bib file are all named after the package title and only differ in the file extension.
• The package version in the POSEIDON.yml file is 1.0.0.
• The poseidonVersion of the package in the POSEIDON.yml file is set to the latest version of the Poseidon schema.
• The POSEIDON.yml file contains the corresponding checksums for the fields genoFile, snpFile, indFile, jannoFile and bibFile.
• There is either no CHANGELOG file or one with a single entry for version 1.0.0.

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• The Publication column in the .janno file is filled and the respective .bib file has complete entries for the listed mentioned keys.
• The .janno file does not include any empty columns or columns only filled with n/a.
• The order of columns in the .janno file adheres to the standard order as defined in the Poseidon schema here.
• 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).

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• The package passes a validation with trident validate --fullGeno.

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• 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).

[stschiff]

Is this ready for review yet?

[stschiff]

Comments from Meeting on January 7th:

• Carbon dates -> Please fill C14 columns for now, and leave calibrated ones empty before we make the next decision
• For samples already published in 2015, make sure you give new Poseidon-IDs, for example <Old_ID>_2023 or so, and then use the Relation_To fields to link.

[stschiff]

I've converted that to a draft for now. Please let us know when you're ready.

[stschiff]

OK, we discussed today that you complete all the first-degree relationships. And please add a Relationship_Note to all samples saying that only first-degree relationships are complete.

[nevrome]

@93Boy Please remember this open ToDo. I hope you still have time for it 👍

[nevrome]

This package is in an intermediate state. Much .janno information is filled, but not everything that should be (relatively) easily available. Some columns need some tweaking to fully fit to the schema. The POSEIDON.yml file is only partially filled.

Ideally somebody would take ownership here and bring the package to a level where it can be reviewed. I will add a Help wanted tag and post in some chats.

[nevrome]

@Tlkhi helped me fix some more details. I think it's ready and will merge now.