Added nf-test for picard/sortsam

modules/nf-core/picard/sortsam/tests/main.nf.test

@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_SORTSAM"
+    script "../main.nf"
+    process "PICARD_SORTSAM"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/sortsam"
+
+    test("test-picard-sortsam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                ]
+				input[1] = "queryname"
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/picard/sortsam/tests/main.nf.test.snap

@@ -0,0 +1,15 @@
+{
+    "test-picard-sortsam": {
+        "content": [
+            "b9847fed94d2b7286e18caaa099658ce",
+            [
+                "versions.yml:md5,f53876b7c58b5aa1564606f3c9c34108"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T09:23:48.485054"
+    }
+}

modules/nf-core/picard/sortsam/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: PICARD_SORTSAM {
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+}

tests/config/pytest_modules.yml

@@ -1073,9 +1073,6 @@ picard/renamesampleinvcf:
 picard/scatterintervalsbyns:
   - modules/nf-core/picard/scatterintervalsbyns/**
   - tests/modules/nf-core/picard/scatterintervalsbyns/**
-picard/sortsam:
-  - modules/nf-core/picard/sortsam/**
-  - tests/modules/nf-core/picard/sortsam/**
 picard/sortvcf:
   - modules/nf-core/picard/sortvcf/**
   - tests/modules/nf-core/picard/sortvcf/**