[ADD] subgenome info

DessimozLab · Dec 19, 2024 · 1f09766 · 1f09766
1 parent 0e8482a
commit 1f09766
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/modules/local/darwin_extract/main.nf b/modules/local/darwin_extract/main.nf
@@ -32,7 +32,7 @@ process CONVERT_PROTEINS {
     container "dessimozlab/omadarwin:nf-latest"
 
     input:
-        tuple val(genome), path(dbpath)
+        tuple val(genome), path(dbpath), path(subgenome)
 
     output:
         path "${genome.UniProtSpeciesCode}.json",   emit: prot_json
@@ -44,6 +44,8 @@ process CONVERT_PROTEINS {
           dbpath := '${dbpath}';
           tot_entries := ${genome.TotEntries};
           tot_aa := ${genome.TotAA};
+          is_polyploid := '${genome.IsPolyploid}';
+          subgenome_path := '${subgenome}';
 
           ReadProgram('\${CODE_REPOS_ROOT}/pyoma/pyoma/browser/build/convert_database.drw');
           done

diff --git a/subworkflows/local/extract_darwin/main.nf b/subworkflows/local/extract_darwin/main.nf
@@ -12,12 +12,13 @@ workflow EXTRACT_DARWIN {
         def summaries = genomes_folder / "Summaries.drw"
         def taxonomy = genomes_folder / "taxonomy.sqlite"
         def splice_data = genomes_folder / "Splicings.drw"
+        def subgenome = genomes_folder / "SubGenomes.drw"
         CONVERT_GS(genomes_folder, matrix_file, summaries)
         CONVERT_GS.out.gs_tsv
             | splitCsv(sep: "\t", header: true)
             | map { row ->
                 def dbfile = file(row.DBpath)
-                return tuple( row, dbfile )
+                return tuple( row, dbfile, subgenome )
                 }
             | transpose
             | set { convert_jobs }