fixes and updates

dpark01 · dpark01 · commit cc20967f3760 · 2025-02-27T19:18:47.000-05:00
diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl
@@ -44,7 +44,7 @@ task taxid_to_nextclade_dataset_name {
         maxRetries: 2
     }
     output {
-        String nextclade_dataset_name = read_string("DATASET_NAME")
+        String nextclade_dataset_name = read_string("nextclade_dataset_name.str")
     }    
 }
 
diff --git a/pipes/WDL/workflows/nextclade_single.wdl b/pipes/WDL/workflows/nextclade_single.wdl
@@ -7,7 +7,12 @@ workflow nextclade_single {
         description: "Run Nextclade on a single genome"
     }
 
-    call nextstrain.nextclade_one_sample
+    call nextstrain.taxid_to_nextclade_dataset_name
+
+    call nextstrain.nextclade_one_sample {
+        input:
+            dataset_name = taxid_to_nextclade_dataset_name.nextclade_dataset_name
+    }
 
     output {
         String nextclade_clade    = nextclade_one_sample.nextclade_clade
@@ -17,6 +22,7 @@ workflow nextclade_single {
         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
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -44,7 +44,7 @@ task taxid_to_nextclade_dataset_name {`
`44`	`44`	`maxRetries: 2`
`45`	`45`	`}`
`46`	`46`	`output {`
`47`		`- String nextclade_dataset_name = read_string("DATASET_NAME")`
	`47`	`+ String nextclade_dataset_name = read_string("nextclade_dataset_name.str")`
`48`	`48`	`}`
`49`	`49`	`}`
`50`	`50`
Original file line number	Diff line number	Diff line change
`@@ -7,7 +7,12 @@ workflow nextclade_single {`
`7`	`7`	`description: "Run Nextclade on a single genome"`
`8`	`8`	`}`
`9`	`9`
`10`		`- call nextstrain.nextclade_one_sample`
	`10`	`+ call nextstrain.taxid_to_nextclade_dataset_name`
	`11`	`+`
	`12`	`+ call nextstrain.nextclade_one_sample {`
	`13`	`+ input:`
	`14`	`+ dataset_name = taxid_to_nextclade_dataset_name.nextclade_dataset_name`
	`15`	`+ }`
`11`	`16`
`12`	`17`	`output {`
`13`	`18`	`String nextclade_clade = nextclade_one_sample.nextclade_clade`
`@@ -17,6 +22,7 @@ workflow nextclade_single {`
`17`	`22`	`String nextclade_aa_dels = nextclade_one_sample.aa_dels_csv`
`18`	`23`	`String nextclade_shortclade = nextclade_one_sample.nextclade_shortclade`
`19`	`24`	`String nextclade_subclade = nextclade_one_sample.nextclade_subclade`
	`25`	`+ String nextclade_pango = nextclade_one_sample.nextclade_pango`
`20`	`26`	`String nextclade_version = nextclade_one_sample.nextclade_version`
`21`	`27`	`}`
`22`	`28`	`}`