Merge pull request #1280 from adamrtalbot/dev

Reorganise pipeline tests into flat structure
nf-core · Apr 10, 2024 · 5833810 · 5833810
2 parents f3aec8b + c259f30
commit 5833810
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Showing 17 changed files with 60 additions and 103 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -64,6 +64,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1266](https://github.com/nf-core/rnaseq/pull/1266) - Delete unecessary tags from nf.test files for modules and subworkflows
 - [PR #1253](https://github.com/nf-core/rnaseq/pull/1253) - Use nf-test files as matrix to test over in CI/CD for efficiency
 - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
+- [PR ####](https://github.com/nf-core/rnaseq/pull/####) - Reorganise pipeline level tests into flat directory structure
 
 ### Parameters
 

diff --git a/nf-test.config b/nf-test.config
@@ -6,7 +6,7 @@ config {
     workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // Location of an optional nextflow.config file specific for executing pipeline tests
-    configFile "tests/config/nextflow.config"
+    configFile "tests/nextflow.config"
 
     profile "test"
 }
diff --git a/...ows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test b/...ows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test
@@ -8,10 +8,6 @@ nextflow_workflow {
 
         when {
             params {
-                // parameters copied from test profile.
-                // We should be able to automatically import these somehow.
-                input = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv"
-
                 // Genome references
                 fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta"
                 gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz"

diff --git a/tests/tests/default/main.nf.test → tests/default.main.nf.test b/tests/tests/default/main.nf.test → tests/default.main.nf.test
@@ -1,7 +1,7 @@
 nextflow_pipeline {
 
-    name "Test pipeline"
-    script "../../../main.nf"
+    name "Test pipeline with default settings"
+    script "../main.nf"
     tag "rnaseq"
     tag "PIPELINE"
 
@@ -10,7 +10,6 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
             }
         }
 

diff --git a/tests/tests/default/main.nf.test.snap → tests/default.main.nf.test.snap b/tests/tests/default/main.nf.test.snap → tests/default.main.nf.test.snap
diff --git a/tests/tests/featurecounts/main.nf.test → tests/featurecounts.main.nf.test b/tests/tests/featurecounts/main.nf.test → tests/featurecounts.main.nf.test
@@ -1,7 +1,7 @@
 nextflow_pipeline {
 
-    name "Test pipeline"
-    script "../../../main.nf"
+    name "Test pipeline with featureCounts with group type false"
+    script "../main.nf"
     tag "rnaseq"
     tag "PIPELINE"
 
@@ -10,7 +10,6 @@ nextflow_pipeline {
         when {
             params {
                 outdir        = "$outputDir"
-                input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
                 featurecounts_group_type = false
             }
         }

diff --git a/tests/kallisto.main.nf.nf.test b/tests/kallisto.main.nf.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test pipeline using Kallisto"
+    script "../main.nf"
+    tag "rnaseq"
+    tag "PIPELINE"
+
+    test("Default profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                pseudo_aligner = 'kallisto'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+    }
+}
diff --git a/tests/tests/min_mapped_reads/main.nf.test → tests/min_mapped_reads.main.nf.test b/tests/tests/min_mapped_reads/main.nf.test → tests/min_mapped_reads.main.nf.test
@@ -1,7 +1,7 @@
 nextflow_pipeline {
 
-    name "Test pipeline"
-    script "../../../main.nf"
+    name "Test pipeline with min_mapped_reads = 90"
+    script "../main.nf"
     tag "rnaseq"
     tag "PIPELINE"
 
@@ -10,7 +10,6 @@ nextflow_pipeline {
         when {
             params {
                 outdir           = "$outputDir"
-                input            = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
                 min_mapped_reads = 90
             }
         }

diff --git a/tests/config/nextflow.config → tests/nextflow.config b/tests/config/nextflow.config → tests/nextflow.config
diff --git a/tests/tests/remove_ribo_rna/main.nf.test → tests/remove_ribo_rna.main.nf.test b/tests/tests/remove_ribo_rna/main.nf.test → tests/remove_ribo_rna.main.nf.test
@@ -1,7 +1,7 @@
 nextflow_pipeline {
 
-    name "Test pipeline"
-    script "../../../main.nf"
+    name "Test pipeline with ribosomal RNA removal"
+    script "../main.nf"
     tag "rnaseq"
     tag "PIPELINE"
 
@@ -10,7 +10,6 @@ nextflow_pipeline {
         when {
             params {
                 outdir          = "$outputDir"
-                input           = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
                 remove_ribo_rna = true
             }
         }

diff --git a/tests/salmon.main.nf.test b/tests/salmon.main.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test pipeline using Salmon"
+    script "../main.nf"
+    tag "rnaseq"
+    tag "PIPELINE"
+
+    test("Default profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                pseudo_aligner = 'salmon'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+    }
+}
diff --git a/tests/tests/skip_qc/main.nf.test → tests/skip_qc.main.nf.test b/tests/tests/skip_qc/main.nf.test → tests/skip_qc.main.nf.test
@@ -1,7 +1,7 @@
 nextflow_pipeline {
 
-    name "Test pipeline"
-    script "../../../main.nf"
+    name "Test pipeline with QC disabled"
+    script "../main.nf"
     tag "rnaseq"
     tag "PIPELINE"
 
@@ -10,7 +10,6 @@ nextflow_pipeline {
         when {
             params {
                 outdir        = "$outputDir"
-                input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
                 skip_qc       = true
             }
         }

diff --git a/tests/tests/skip_trimming/main.nf.test → tests/skip_trimming.main.nf.test b/tests/tests/skip_trimming/main.nf.test → tests/skip_trimming.main.nf.test
@@ -1,7 +1,7 @@
 nextflow_pipeline {
 
-    name "Test pipeline"
-    script "../../../main.nf"
+    name "Test pipeline with trimming disabled"
+    script "../main.nf"
     tag "rnaseq"
     tag "PIPELINE"
 
@@ -10,7 +10,6 @@ nextflow_pipeline {
         when {
             params {
                 outdir        = "$outputDir"
-                input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
                 skip_qc       = true
             }
         }

diff --git a/tests/tests/kallisto/main.nf.test b/tests/tests/kallisto/main.nf.test
diff --git a/tests/tests/kallisto/main.nf.test.snap b/tests/tests/kallisto/main.nf.test.snap
diff --git a/tests/tests/salmon/main.nf.test b/tests/tests/salmon/main.nf.test
diff --git a/tests/tests/salmon/main.nf.test.snap b/tests/tests/salmon/main.nf.test.snap