Changes in pipeline to account for multiple assemblies

files/ftp-export/genome_coordinates/known-coordinates.sql

@@ -4,4 +4,5 @@ select distinct
   assembly.ensembl_url,
   assembly.taxid
 from ensembl_assembly assembly
+where assembly.selected_genome = true
 ) TO STDOUT CSV

files/genes/species.sql

@@ -2,4 +2,5 @@ COPY (
   select
     distinct assembly_id, taxid
   from ensembl_assembly
+  where selected_genome = true
 ) TO STDOUT CSV

files/genome-mapping/find_species.sql

@@ -7,4 +7,5 @@ COPY (
   FROM ensembl_assembly
   WHERE
     division NOT IN ('EnsemblProtists', 'EnsemblFungi')
+    AND selected_genome = true
 ) TO STDOUT CSV;

files/import-data/post-release/001__coordinate-systems.sql

@@ -17,6 +17,7 @@ SELECT
   load.karyotype_rank
 FROM load_coordinate_info load
 JOIN ensembl_assembly ensembl ON ensembl.assembly_id = load.assembly_id
+WHERE ensembl.selected_genome = true
 )
 ON CONFLICT (chromosome, assembly_id) DO UPDATE
 SET

files/import-data/post-release/001__ensembl-pseudogenes.sql

@@ -25,6 +25,7 @@ from load_ensembl_pseudogenes load
 join ensembl_assembly assem
 on
   assem.assembly_id = load.assembly_id
+where assem.selected_genome = true
 ) ON CONFLICT (md5(region_name)) DO NOTHING;
 
 INSERT INTO ensembl_pseudogene_exons (

files/import-data/post-release/001__locations.sql

@@ -27,6 +27,8 @@ on
     assembly.assembly_id = load.assembly_id
 WHERE
   load.chromosome is not null
+AND
+  assembly.selected_genome = true
 ON CONFLICT (accession, name, local_start, local_end, assembly_id)
 DO NOTHING
 ;

files/repeats/find-assemblies.sql

@@ -7,5 +7,5 @@ FROM ensembl_assembly species
 WHERE
   exists(select 1 from rnc_sequence_regions reg where reg.assembly_id = species.assembly_id)
   and species.division != 'EnsemblFungi'
+  and species.selected_genome = true
 ) TO STDOUT CSV;
-

workflows/databases/mirgenedb.nf

@@ -7,7 +7,7 @@ process mirgenedb {
   """
   scp $params.databases.mirgenedb.remote mirgenedb.json
   psql \
-    --command='COPY (select assembly_id,assembly_ucsc from ensembl_assembly where assembly_ucsc is not null) TO STDOUT (FORMAT CSV)' \
+    --command='COPY (select assembly_id,assembly_ucsc from ensembl_assembly where assembly_ucsc is not null and selected_genome = true) TO STDOUT (FORMAT CSV)' \
     "$PGDATABASE" > assemblies.tsv
   rnac mirgenedb parse assemblies.tsv mirgenedb.json .
   """