nf-test migration (#4113)

nf-core · Oct 18, 2023 · 977d17c · 977d17c
1 parent 15b935d
commit 977d17c
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Showing 5 changed files with 119 additions and 4 deletions.
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_SORT"
+    script "../main.nf"
+    process "SAMTOOLS_SORT"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/sort"
+
+    test("test_samtools_sort") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("test_samtools_sort_stub") {
+
+        config "./nextflow.config"
+        options "-stub-run"
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_SORT {
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+
+}
diff --git a/modules/nf-core/samtools/sort/tests/tags.yml b/modules/nf-core/samtools/sort/tests/tags.yml
@@ -0,0 +1,3 @@
+samtools/sort:
+  - modules/nf-core/samtools/sort/**
+  - tests/modules/nf-core/samtools/sort/**
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -3298,10 +3298,6 @@ samtools/reheader:
   - modules/nf-core/samtools/reheader/**
   - tests/modules/nf-core/samtools/reheader/**
 
-samtools/sort:
-  - modules/nf-core/samtools/sort/**
-  - tests/modules/nf-core/samtools/sort/**
-
 samtools/stats:
   - modules/nf-core/samtools/stats/**
   - tests/modules/nf-core/samtools/stats/**