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Add 2023_Ferraz_NatureEcologyEvolution #27

Merged
merged 17 commits into from
Feb 13, 2025
Merged

Add 2023_Ferraz_NatureEcologyEvolution #27

merged 17 commits into from
Feb 13, 2025

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TCLamnidis
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@TCLamnidis TCLamnidis commented Nov 22, 2024 •
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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

@TCLamnidis TCLamnidis added the help wanted Extra attention is needed label Nov 22, 2024
@Kavlahkaff
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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?

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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.

Kavlahkaff and others added 11 commits November 28, 2024 17:08
@Kavlahkaff
filled janno
395af14
@TCLamnidis
Update 2023_Ferraz_NatureEcologyEvolution. merge TF and MT data.
1aa852f
@TCLamnidis
Remove duplicate entires. update MNT-produced metadata
2261ee1
@TCLamnidis
Merge branch 'add_2023_Ferraz_NatureEcologyEvolution' into add_2023_F…
8c0db5f 
…erraz_NatureEcologyEvolution
@TCLamnidis
Update 2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEv…
323d137 
…olution.janno
@TCLamnidis
Merge pull request #30 from Kavlahkaff/add_2023_Ferraz_NatureEcologyE…
1e66984 
…volution

.janno for 2023_Ferraz_NatureEvolution
@TCLamnidis
Merge branch 'main' into add_2023_Ferraz_NatureEcologyEvolution
b7bdabb
@TCLamnidis
Add janno info collected by @Kavlahkaff. Mirror info to fam file.Add @…
a28f2be 
…Kavlahkaff as Contributor.
@TCLamnidis
update checksums
dad727a
@TCLamnidis
bump version. update changelog
a5d58b5
@TCLamnidis
Add bibFile and Publication info.
4891a8a
@TCLamnidis TCLamnidis added the Final review needed This PR needs its final review before going live label Dec 20, 2024
@TCLamnidis
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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

@TCLamnidis TCLamnidis mentioned this pull request Dec 20, 2024
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stschiff commented Jan 6, 2025

Yes, I think this is because the sequence-formats library doesn't use Unicode (shame on the developer). I am not sure when I can fix that, but until then I recommend avoiding non-ASCII characters in group and individual-names.

@stschiff stschiff mentioned this pull request Jan 6, 2025
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@stschiff stschiff assigned TCLamnidis and unassigned Kavlahkaff Jan 14, 2025
@TCLamnidis TCLamnidis removed the help wanted Extra attention is needed label Jan 28, 2025
@TCLamnidis TCLamnidis requested review from stschiff, nevrome and AyGhal and removed request for nevrome January 29, 2025 14:24
@TCLamnidis TCLamnidis removed the request for review from AyGhal February 4, 2025 13:43
@TCLamnidis
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@stschiff Please rereview.

stschiff
stschiff approved these changes Feb 12, 2025
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Great. Looks all good. You could consider removing empty columns from the Janno, using the new trident rectify --jannoRemoveEmpty feature. I think that's cleaner, and in the Community Archive we now also require it.

@TCLamnidis TCLamnidis merged commit 71363ce into main Feb 13, 2025
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@TCLamnidis TCLamnidis deleted the add_2023_Ferraz_NatureEcologyEvolution branch February 13, 2025 12:57
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