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154 add gnn outputs into color ssn#155

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nilsoberg merged 11 commits into
nextflow-testfrom
154-add-gnn-outputs-into-color-ssn
Apr 18, 2025
Merged

154 add gnn outputs into color ssn#155
nilsoberg merged 11 commits into
nextflow-testfrom
154-add-gnn-outputs-into-color-ssn

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@nilsoberg nilsoberg commented Apr 11, 2025

Added GNN outputs to the color SSN. This required a significant refactoring of the way SSNs were processed in the shared Color SSN pipeline. Additionally, the missing pieces for the GNDs were added (by necessity for the new node attributes). This should not conflict with existing PRs.

- Post-processes colored SSN to insert GNT data
- GNT data (present/neighbors/ID/neighbor families) is added after cluster number
- Data comes from GND
- GND schema moved to separate module and GND reader created so that updated pipeline can use data
- Move coloring to script in each pipeline
- Colors assigned in the shared color workflow
- This allows the GNT pipeline to process the SSN only once instead of twice
  (once by the color SSN shared pipeline and once in the GNT to add the GNT
  attributes
@nilsoberg nilsoberg linked an issue Apr 11, 2025 that may be closed by this pull request
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Approved with very minor comments and questions.

I sound like a broken record in my comments. I think I caught the different areas of the codes where UniRef functionality is to be added for the GNT. Is documentation of those spots important for the #111 issue (or sub-issues that might spawn from there)?

Comment thread lib/EFI/GNT/GND.pm Outdated
Comment thread lib/EFI/Annotations.pm
Comment thread lib/EFI/Annotations.pm Outdated
Comment thread lib/EFI/GNT/GND.pm
Comment thread lib/EFI/GNT/GND.pm
Comment thread pipelines/gnt/create_gnns.pl Outdated
Comment thread pipelines/gnt/create_gnns.pl
Comment thread pipelines/gnt/color_gnt_xgmml.pl Outdated
Comment thread pipelines/gnd/create_gnd.pl
Comment thread pipelines/shared/perl/assign_cluster_colors.pl Outdated
@nilsoberg nilsoberg merged commit a210f3d into nextflow-test Apr 18, 2025
@nilsoberg nilsoberg deleted the 154-add-gnn-outputs-into-color-ssn branch April 18, 2025 19:26
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Add GNN outputs into Color SSN

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