update utils subworkflows

subworkflows/nf-core/utils_nextflow_pipeline/main.nf

@@ -4,6 +4,7 @@
 
 import org.yaml.snakeyaml.Yaml
 import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
 
 /*
 ========================================================================================
@@ -16,7 +17,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     take:
     print_version        // bool
     dump_parameters      // bool
-    output_directory     // path: base directory used to publish pipeline results
+    outdir               // path: base directory used to publish pipeline results
     check_conda_channels // bool
 
     main:
@@ -32,8 +33,8 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     //
     // Dump pipeline parameters to a JSON file
     //
-    if (dump_parameters && output_directory) {
-        dumpParametersToJSON(output_directory)
+    if (dump_parameters && outdir) {
+        dumpParametersToJSON(outdir)
     }
 
     //
@@ -42,9 +43,6 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     if (check_conda_channels) {
         checkCondaChannels()
     }
-
-    emit:
-        out = true
 }
 
 /*
@@ -74,16 +72,15 @@ def getWorkflowVersion() {
 //
 // Dump pipeline parameters to a JSON file
 //
-def dumpParametersToJSON(output_directory) {
-    def output_d = new File("${output_directory}/pipeline_info/")
-    if (!output_d.exists()) {
-        output_d.mkdirs()
-    }
-
+def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    def output_pf  = new File(output_d, "params_${timestamp}.json")
+    def filename   = "params_${timestamp}.json"
+    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
     def jsonStr    = JsonOutput.toJson(params)
-    output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+
+    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    temp_pf.delete()
 }
 
 //

subworkflows/nf-core/utils_nextflow_pipeline/meta.yml

@@ -24,14 +24,11 @@ input:
       type: boolean
       description: |
         Check if the conda channel priority is correct.
-output:
-  - out:
-      type: boolean
-      description: |
-        Dummy output for making using in process chaining.
+output: []
 authors:
   - "@adamrtalbot"
   - "@drpatelh"
 maintainers:
   - "@adamrtalbot"
   - "@drpatelh"
+  - "@maxulysse"

subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test → subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test

@@ -12,22 +12,12 @@ nextflow_function {
 
         function "getWorkflowVersion"
 
-        when {
-            function {
-                """
-                // no inputs
-                """
-            }
-        }
-
         then {
             assert function.success
             assert snapshot(function.result).match()
         }
-
     }
 
-
     test("Test Function dumpParametersToJSON") {
 
         function "dumpParametersToJSON"
@@ -43,29 +33,16 @@ nextflow_function {
 
         then {
             assert function.success
-            assert function.result =~ /publish_dir_mode/
-            assert function.result =~ /copy/
         }
-
     }
-	
+
     test("Test Function checkCondaChannels") {
 
         function "checkCondaChannels"
 
-        when {
-            function {
-                """
-                // no inputs
-                """
-            }
-        }
-
         then {
             assert function.success
             assert snapshot(function.result).match()
         }
-
     }
-
 }

subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test

@@ -26,9 +26,7 @@ nextflow_workflow {
 
         then {
             assert workflow.success
-            assert snapshot(workflow.out).match()
         }
-
     }
 
     test("Should print version") {
@@ -51,10 +49,8 @@ nextflow_workflow {
             assert workflow.success
             assert workflow.stdout.contains("nextflow_workflow v9.9.9")
         }
-
     }
 
-
     test("Should dump params") {
 
         when {
@@ -73,9 +69,7 @@ nextflow_workflow {
 
         then {
             assert workflow.success
-            assert snapshot(workflow.out).match()
         }
-
     }
 
     test("Should not create params JSON if no output directory") {
@@ -96,9 +90,6 @@ nextflow_workflow {
 
         then {
             assert workflow.success
-            assert snapshot(workflow.out, path(params.outdir).list()).match()
         }
-
     }
-
 }