improvements

Author: dpark01

pipes/WDL/tasks/tasks_nextstrain.wdl

@@ -14,6 +14,8 @@ task taxid_to_nextclade_dataset_name {
         mkdir -p taxdump
         read_utils.py extract_tarball "~{taxdump_tgz}" taxdump
 
+        touch nextclade_dataset_name.str
+
         python3 << CODE
         import csv
         import metagenomics

pipes/WDL/workflows/nextclade_single.wdl

@@ -9,20 +9,27 @@ workflow nextclade_single {
 
     call nextstrain.taxid_to_nextclade_dataset_name
 
-    call nextstrain.nextclade_one_sample {
-        input:
-            dataset_name = taxid_to_nextclade_dataset_name.nextclade_dataset_name
+    if (defined(taxid_to_nextclade_dataset_name.nextclade_dataset_name) 
+        && taxid_to_nextclade_dataset_name.nextclade_dataset_name != "") {
+
+        String dataset = taxid_to_nextclade_dataset_name.nextclade_dataset_name
+
+        call nextstrain.nextclade_one_sample {
+            input:
+                dataset_name = dataset
+        }
     }
 
     output {
-        String nextclade_clade    = nextclade_one_sample.nextclade_clade
-        File   nextclade_tsv      = nextclade_one_sample.nextclade_tsv
-        File   nextclade_json     = nextclade_one_sample.nextclade_json
-        String nextclade_aa_subs  = nextclade_one_sample.aa_subs_csv
-        String nextclade_aa_dels  = nextclade_one_sample.aa_dels_csv
-        String nextclade_shortclade = nextclade_one_sample.nextclade_shortclade
-        String nextclade_subclade = nextclade_one_sample.nextclade_subclade
-        String nextclade_pango    = nextclade_one_sample.nextclade_pango
-        String nextclade_version  = nextclade_one_sample.nextclade_version
+        String? nextclade_dataset  = dataset
+        String? nextclade_clade    = nextclade_one_sample.nextclade_clade
+        File?   nextclade_tsv      = nextclade_one_sample.nextclade_tsv
+        File?   nextclade_json     = nextclade_one_sample.nextclade_json
+        String? nextclade_aa_subs  = nextclade_one_sample.aa_subs_csv
+        String? nextclade_aa_dels  = nextclade_one_sample.aa_dels_csv
+        String? nextclade_shortclade = nextclade_one_sample.nextclade_shortclade
+        String? nextclade_subclade = nextclade_one_sample.nextclade_subclade
+        String? nextclade_pango    = nextclade_one_sample.nextclade_pango
+        String? nextclade_version  = nextclade_one_sample.nextclade_version
     }
 }