swap to nextflow config

nf-core · Nov 21, 2024 · 2023aef · 2023aef
1 parent 244a072
commit 2023aef
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Showing 3 changed files with 10 additions and 11 deletions.
diff --git a/modules/nf-core/parabricks/deepvariant/tests/gvcf.config b/modules/nf-core/parabricks/deepvariant/tests/gvcf.config
diff --git a/modules/nf-core/parabricks/deepvariant/tests/main.nf.test b/modules/nf-core/parabricks/deepvariant/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_process {
 
     test("human - bam - intervals") {
 
-        config './copy.config'
+        config './nextflow.config'
 
         when {
             process {
@@ -75,9 +75,12 @@ nextflow_process {
 
     test("human - bam - intervals - gvcf") {
 
-        config './gvcf.config'
+        config './nextflow.config'
 
         when {
+            params {
+                 module_args = '--gvcf'
+            }
             process {
                 """
                 input[0] = [
@@ -139,10 +142,13 @@ nextflow_process {
 
     test("human - bam - intervals - gvcf - stub") {
 
-        config './gvcf.config'
+        config './nextflow.config'
         options "-stub"
 
         when {
+            params {
+                 module_args = '--gvcf'
+            }
             process {
                 """
                 input[0] = [

diff --git a/.../parabricks/deepvariant/tests/copy.config → ...abricks/deepvariant/tests/nextflow.config b/.../parabricks/deepvariant/tests/copy.config → ...abricks/deepvariant/tests/nextflow.config
@@ -1,6 +1,7 @@
 process {
 
     withName: 'PARABRICKS_DEEPVARIANT' {
+        ext.args = params.module_args
         stageInMode = 'copy'
     }