drop zero length assemblies

broadinstitute · Sep 18, 2024 · 9017298 · 9017298
1 parent 7bbfee4
commit 9017298
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
@@ -150,15 +150,17 @@ workflow scaffold_and_refine_multitaxa {
             "sample":              '{"entityType":"sample","entityName":"' + sample_id + '"}'
         }
 
-        scatter(h in assembly_header) {
-            String stat_by_taxon = stats_by_taxon[h]
+        if(assembly_length_unambiguous > min_scaffold_unambig) {
+            scatter(h in assembly_header) {
+                String stat_by_taxon = stats_by_taxon[h]
+            }
         }
     }
 
     ### summary stats
     call utils.concatenate {
       input:
-        infiles     = [write_tsv([assembly_header]), write_tsv(stat_by_taxon)],
+        infiles     = [write_tsv([assembly_header]), write_tsv(select_all(stat_by_taxon))],
         output_name = "assembly_metadata-~{sample_id}.tsv"
     }