Add secret to the Nextflow helper script

lazappi · lazappi · commit 4fcf7c2a7840 · 2026-05-13T16:33:39.000+02:00
diff --git a/src/main/resources/io/viash/runners/nextflow/VDSL3Helper.nf b/src/main/resources/io/viash/runners/nextflow/VDSL3Helper.nf
@@ -159,9 +159,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
     }
   }
 
-  // multiple entries allowed: label, publishdir
+  // multiple entries allowed: label, publishdir, secret
   def drctvStrs = drctv.collect { key, value ->
-    if (key in ["label", "publishDir"]) {
+    if (key in ["label", "publishDir", "secret"]) {
       value.collect{ val ->
         if (val instanceof Map) {
           "\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ")

Original file line number	Diff line number	Diff line change
`@@ -159,9 +159,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {`
`159`	`159`	`}`
`160`	`160`	`}`
`161`	`161`
`162`		`- // multiple entries allowed: label, publishdir`
	`162`	`+ // multiple entries allowed: label, publishdir, secret`
`163`	`163`	`def drctvStrs = drctv.collect { key, value ->`
`164`		`- if (key in ["label", "publishDir"]) {`
	`164`	`+ if (key in ["label", "publishDir", "secret"]) {`
`165`	`165`	`value.collect{ val ->`
`166`	`166`	`if (val instanceof Map) {`
`167`	`167`	`"\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ")`