Reorganise and rename tests

CHANGELOG.md

@@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#276](https://github.com/nf-core/phaseimpute/pull/276) - Migrate all `params.value` usage to entry workflow. Use groovy map to store parameters for each step. Use nextflow 25.10 for `getGenomeAttribute()`.
 - [#286](https://github.com/nf-core/phaseimpute/pull/286) - Remove unecessary `saveAs` from config thanks to topic migration.
 - [#291](https://github.com/nf-core/phaseimpute/pull/291) - Update TEMPLATE to nf-core tools version 4.0.2.
+- [#292](https://github.com/nf-core/phaseimpute/pull/292) - Reorganise and rename pipeline level tests.
 
 ### `Fixed`
 

workflows/phaseimpute/main.nf

@@ -128,7 +128,7 @@ workflow PHASEIMPUTE {
         .count()
 
     ch_map_branched = ch_map
-        .branch { meta, map_file ->
+        .branch { _meta, map_file ->
             non_empty: map_file
             empty: true
         }
@@ -308,7 +308,7 @@ workflow PHASEIMPUTE {
     //
     if (steps.contains("impute") || steps.contains("all")) {
 
-        if (params.tools.split(',').any{ it in ["stitch", "quilt"] }) {
+        if (tools.any{ tool -> tool in ["stitch", "quilt"] }) {
             // Transform posfile to tabulated format shared by QUILT and STITCH
             GAWK_POSFILE_IMPUTE(
                 ch_posfile.map{

workflows/phaseimpute/tests/test_all.nf.test

@@ -8,14 +8,15 @@ nextflow_pipeline {
 
     config "./nextflow.config"
 
-    test("Check test_all - with map") {
+    test("Check test_all - no map - no chunks") {
         config "../../../conf/test_all.config"
         when {
             params {
                 publish_dir_mode = "copy"
                 pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/'
                 outdir = "$outputDir"
                 publish_all = true
+                map = null
             }
         }
 
@@ -35,15 +36,14 @@ nextflow_pipeline {
         }
     }
 
-    test("Check test_all - no map") {
+    test("Check test_all - with map - no chunks") {
         config "../../../conf/test_all.config"
         when {
             params {
                 publish_dir_mode = "copy"
                 pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/'
                 outdir = "$outputDir"
                 publish_all = true
-                map = null
             }
         }
 

workflows/phaseimpute/tests/test_beagle5.nf.test

@@ -8,13 +8,15 @@ nextflow_pipeline {
 
     config "./nextflow.config"
 
-    test("Check test_beagle5 - with chunks - with map") {
+    test("Check test_beagle5 - no map - no chunks") {
         config "../../../conf/test_beagle5.config"
         when {
             params {
                 publish_dir_mode = "copy"
                 pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/'
                 outdir = "$outputDir"
+                chunks = null
+                map = null
                 publish_all = true
             }
         }
@@ -30,15 +32,13 @@ nextflow_pipeline {
         }
     }
 
-    test("Check test_beagle5 - no chunks - no map") {
+    test("Check test_beagle5 - with map - with chunks") {
         config "../../../conf/test_beagle5.config"
         when {
             params {
                 publish_dir_mode = "copy"
                 pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/'
                 outdir = "$outputDir"
-                chunks = null
-                map = null
                 publish_all = true
             }
         }

workflows/phaseimpute/tests/test_dog.nf.test

@@ -8,7 +8,7 @@ nextflow_pipeline {
 
     config "./nextflow.config"
 
-    test("Check test_dog - no map") {
+    test("Check test_dog - no map - no chunks") {
         config "../../../conf/test_dog.config"
         when {
             params {

workflows/phaseimpute/tests/test_dog.nf.test.snap

@@ -1,5 +1,5 @@
 {
-    "Check test_dog - no map": {
+    "Check test_dog - no map - no chunks": {
         "content": [
             {
                 "workflow size": 91,

workflows/phaseimpute/tests/test_glimpse1.nf.test

@@ -8,13 +8,15 @@ nextflow_pipeline {
 
     config "./nextflow.config"
 
-    test("Check test_glimpse1 - with chunks - with map") {
+    test("Check test_glimpse1 - no map - no chunks") {
         config "../../../conf/test.config"
         when {
             params {
                 publish_dir_mode = "copy"
                 pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/'
                 outdir = "$outputDir"
+                chunks = null
+                map = null
                 publish_all = true
             }
         }
@@ -30,15 +32,13 @@ nextflow_pipeline {
         }
     }
 
-    test("Check test_glimpse1 - no chunks - no map") {
+    test("Check test_glimpse1 - with map - with chunks") {
         config "../../../conf/test.config"
         when {
             params {
                 publish_dir_mode = "copy"
                 pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/'
                 outdir = "$outputDir"
-                chunks = null
-                map = null
                 publish_all = true
             }
         }