Added nf-test for picard/bedtointervallist (#6298)

nf-core · Aug 26, 2024 · 8c4124c · 8c4124c
1 parent f5bc694
commit 8c4124c
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Showing 6 changed files with 75 additions and 34 deletions.
diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_BEDTOINTERVALLIST"
+    script "../main.nf"
+    process "PICARD_BEDTOINTERVALLIST"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/bedtointervallist"
+
+    test("test-picard-bedtointervallist") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
+				]
+				input[1] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+				]
+				input[2] = []
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "test-picard-bedtointervallist": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
+                ],
+                "interval_list": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:39:08.82372"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -941,9 +941,6 @@ peka:
 phyloflash:
   - modules/nf-core/phyloflash/**
   - tests/modules/nf-core/phyloflash/**
-picard/bedtointervallist:
-  - modules/nf-core/picard/bedtointervallist/**
-  - tests/modules/nf-core/picard/bedtointervallist/**
 picard/cleansam:
   - modules/nf-core/picard/cleansam/**
   - tests/modules/nf-core/picard/cleansam/**

diff --git a/tests/modules/nf-core/picard/bedtointervallist/main.nf b/tests/modules/nf-core/picard/bedtointervallist/main.nf
diff --git a/tests/modules/nf-core/picard/bedtointervallist/nextflow.config b/tests/modules/nf-core/picard/bedtointervallist/nextflow.config
diff --git a/tests/modules/nf-core/picard/bedtointervallist/test.yml b/tests/modules/nf-core/picard/bedtointervallist/test.yml