Add 2023_Ferraz_NatureEcologyEvolution

[TCLamnidis]

Adds/Updates 2023_Ferraz_NatureEcologyEvolution

Linked to poseidon-framework/minotaur-recipes#4

New packages added to the minotaur archive are always published in version 1.0.0. This means that nay and all changes made to the package during the review process, should only bump the Minor or Patch version of the package.

PR checklist:

• This package contains a BibTex file.
• If this package already exists in the community archive:
  • The information from the community archive was used to fill-in empty janno fields.
  • The commands used for the fill-in and any tool versions are kept track of in the README file.
• Country information is also present in the Country_ISO column.

Once the Pull Request has passed the review process, ensure the pacakge version is bumped once more before publishing with:

trident rectify -d <package_dir> --logText 'Bump version for release' --packageVersionMajor --checksumAll

[Kavlahkaff]

Hey @TCLamnidis,
in the .janno file for there seem to be duplicate entries for every individual which differ in their suffix in the Poseidon ID (_TF vs. _MT). The _MT rows seem to have no values. Is this intentional or should I remove those?

[TCLamnidis]

No. The _TF and _MT suffixes denote if the data is 1240K or mtDNA capture. Effectively each individual is in the dataset twice atm. Hence, it makes sense that the MT data have 0 SNPs, since there is likely little to no data on the autosomes after mtDNA capture.

Please fill in the information of each individual once. I will likely have to reprocess this dataset to combine the MT and TF data, but should still be able to make use of the metadata.

[TCLamnidis]

There is an issue with trident validation, where special characters in the Group_Name (e.g. ç) are not matched to the same characters in the fam/ind file.

trident v1.5.4.0 for poseidon v2.5.0, v2.6.0, v2.7.0, v2.7.1
https://poseidon-framework.github.io

[Info]    Validating: 2023_Ferraz_NatureEcologyEvolution/
[Info]    Checking base directories... 
[Info]    Searching POSEIDON.yml files... 
[Info]    1 found
[Info]    Checking Poseidon versions... 
[Info]    Initializing packages... 
[Warning] Some packages were skipped due to issues:
[Warning] In the package described in 2023_Ferraz_NatureEcologyEvolution/POSEIDON.yml:
[Warning] Cross-file consistency issue in package 2023_Ferraz_NatureEcologyEvolution: Individual GroupID mismatch between genotype data (left) and .janno files (right). Note that this could be due to a wrong Plink file population-name encoding (see the --inPlinkPopName option). (Cabeçuda = Cabeçuda), (Cabeçuda = Cabeçuda), (CubatãoI = CubatãoI), (CubatãoI = CubatãoI), (Limão = Limão), ...
[Info]    Packages loaded: 0
[Error]   Validation failed