Refactor the nextflow code to handle the auto.publish as a string

viash-io · Oct 10, 2023 · 939d5b5 · 939d5b5
1 parent 5ab3664
commit 939d5b5
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/src/main/resources/io/viash/platforms/nextflow/VDSL3Helper.nf b/src/main/resources/io/viash/platforms/nextflow/VDSL3Helper.nf
@@ -240,7 +240,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   def escapedScript = rawScript.replace('\\', '\\\\').replace('$', '\\$').replace('"""', '\\"\\"\\"')
 
   // publishdir assert
-  def assertStr = (workflowArgs.auto.publish == true) || workflowArgs.auto.transcript ? 
+  def assertStr = (workflowArgs.auto.publish == "true") || workflowArgs.auto.transcript ? 
     """\nassert task.publishDir.size() > 0: "if auto.publish is true, params.publish_dir needs to be defined.\\n  Example: --publish_dir './output/'" """ :
     ""
 

diff --git a/src/main/resources/io/viash/platforms/nextflow/workflowFactory/processAuto.nf b/src/main/resources/io/viash/platforms/nextflow/workflowFactory/processAuto.nf
@@ -18,7 +18,8 @@ def processAuto(Map auto) {
   assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean"
 
   // check auto.publish
-  assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'"
+  assert auto.publish instanceof CharSequence
+  assert auto.publish in ["true", "false", "state"], "auto.publish must be 'true', 'false', or 'state'"
 
   return auto.subMap(expectedKeys)
 }
diff --git a/src/main/resources/io/viash/platforms/nextflow/workflowFactory/processWorkflowArgs.nf b/src/main/resources/io/viash/platforms/nextflow/workflowFactory/processWorkflowArgs.nf
@@ -29,7 +29,7 @@ def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) {
   workflowArgs["auto"] = processAuto(defaultWfArgs.auto + workflowArgs["auto"])
 
   // auto define publish, if so desired
-  if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) {
+  if (workflowArgs.auto.publish == "true" && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) {
     // can't assert at this level thanks to the no_publish profile
     // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : 
     //   "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" +