first draft of the Maslomecz group (IA Wielbark, Poland) dataset for the almost accepted Golubinski 2026 paper in Genome Biology

[martynamolak]

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.

---

• Samples that already have been published previously, and got re-analysed (e.g. re-sequenced) for the now packaged publication, have a modified Poseidon_ID of the form <Original Poseidon_ID>_<Initials of the main author>_<Year>. Re-analysed versions of I1685 (Lazaridis et al. 2016) should, for example, be assigned the IDs I1685_IL22 (Lazaridis et al. 2022) and I1685_IL25 (Lazaridis et al. 2025).

---

• The package is complete and features the following elements:
  • Genotype data in binary PLINK format (not EIGENSTRAT format).
  • Genotype has been provided by the original authors of the publication describing the data.
  • 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.

---

• 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).

---

• The package passes 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).

[martynamolak]

This time for real, as the editor asked for a working link already. Hope it will be possible soon.

[nevrome]

Thank you, Martyna - very nice! The package looks good to me.

I only applied two minor changes to the .janno file:

1. I removed unnecessary leading whitespaces after ; in list columns
2. I turned Endogenous from fractions to percent

If you're OK with these changes in ec5844b then we can merge this. I don't think further review is necessary.

For your next submission please remember to check the boxes in the checklist above.

[martynamolak]

Sorry for the checkboxes. I wasn't sure how that worked and also did the submission quite quickly last night.
Thank you so much again for fasttracking this and handling the review yourself.
If you're good to merge to master, I am too.
Please let me know if I should doo anything or it's all on your side now.

[nevrome]

OK - perfect! Will merge now. Note that https://server.poseidon-adna.org will only get updated tonight.

[nevrome]

Had to test something unrelated and decided to update the server. So the package is there already: https://server.poseidon-adna.org/explorer/community-archive/2026_Golubinski_Maslomecz