Added nf-test for picard/mergesamfiles (#6258)

nf-core · Aug 23, 2024 · 98f19f2 · 98f19f2
1 parent c57b489
commit 98f19f2
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Showing 6 changed files with 54 additions and 29 deletions.
diff --git a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test
@@ -0,0 +1,39 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_MERGESAMFILES"
+    script "../main.nf"
+    process "PICARD_MERGESAMFILES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/mergesamfiles"
+
+    test("test-picard-mergesamfiles") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "test-picard-mergesamfiles": {
+        "content": [
+            "730da54c088350ff625d34b95e623dca",
+            [
+                "versions.yml:md5,3b5243ec10606330dd11a38fa7c7fa1f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T10:50:00.555746"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1112,9 +1112,6 @@ picard/fixmateinformation:
 picard/liftovervcf:
   - modules/nf-core/picard/liftovervcf/**
   - tests/modules/nf-core/picard/liftovervcf/**
-picard/mergesamfiles:
-  - modules/nf-core/picard/mergesamfiles/**
-  - tests/modules/nf-core/picard/mergesamfiles/**
 picard/renamesampleinvcf:
   - modules/nf-core/picard/renamesampleinvcf/**
   - tests/modules/nf-core/picard/renamesampleinvcf/**

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