Changes in pipeline to account for multiple assemblies #132
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I have checked the workflows that use these files and I'm pretty sure the changes are ok The full list of potentially affected files: files/repeats/find-assemblies.sql files/genome-mapping/post.sql files/genome-mapping/find_species.sql files/ftp-export/genome_coordinates/known-coordinates.sql files/genome-mapping/load.ctl files/genes/species.sql files/genes/schema.sql files/import-data/post-release/001__regions.sql files/import-data/post-release/001__coordinate-systems.sql files/import-data/post-release/001__ensembl-pseudogenes.sql files/import-data/post-release/001__locations.sql files/import-data/post-release/002__Cleanup_assembly_table.sql files/import-data/ensembl/known-assemblies.sql files/import-data/pre-release/000__assemblies.sql workflows/databases/mirgenedb.nf rnacentral_pipeline/databases/ensembl/metadata/assemblies.py If one is not touched in this commit, then I think it didn't need modification
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This looks reasonable to me, but what are we doing with the Cleanup_assembly_table script? I think we can just leave the assemblies alone since we will only use the selected_genomes in the webcode. |
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Looked at these files (output of
rg -l ensembl_assembly)files/repeats/find-assemblies.sql
files/genome-mapping/post.sql
files/genome-mapping/find_species.sql
files/ftp-export/genome_coordinates/known-coordinates.sql
files/genome-mapping/load.ctl
files/genes/species.sql
files/genes/schema.sql
files/import-data/post-release/001__regions.sql
files/import-data/post-release/001__coordinate-systems.sql
files/import-data/post-release/001__ensembl-pseudogenes.sql
files/import-data/post-release/001__locations.sql
files/import-data/post-release/002__Cleanup_assembly_table.sql
files/import-data/ensembl/known-assemblies.sql
files/import-data/pre-release/000__assemblies.sql
workflows/databases/mirgenedb.nf
rnacentral_pipeline/databases/ensembl/metadata/assemblies.py
And chased down uses of those files. I think I got everything and it will do what we want