Added nf-test for pairtools/parse

modules/nf-core/pairtools/parse/tests/main.nf.test

@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process PAIRTOOLS_PARSE"
+    script "../main.nf"
+    process "PAIRTOOLS_PARSE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pairtools"
+    tag "pairtools/parse"
+
+    test("test-pairtools-parse") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.sam', checkIfExists: true) ]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.chrom.sizes', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.pairsam[0][1]).linesGzip[3..7],
+					process.out.stat,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/pairtools/parse/tests/main.nf.test.snap

@@ -0,0 +1,30 @@
+{
+    "test-pairtools-parse": {
+        "content": [
+            [
+                "#chromsize: chr1 1000",
+                "#chromsize: chr2 1000",
+                "#samheader: @SQ\tSN:chr1\tLN:1000",
+                "#samheader: @SQ\tSN:chr2\tLN:1000",
+                "#samheader: @PG\tID:mock\tPN:mock\tVN:0.0.0\tCL:mock"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.raw.pairsam.stat:md5,054bf78ee4f0a4c447ad3eeb81f1f4ae"
+                ]
+            ],
+            [
+                "versions.yml:md5,2c8cb00722749f8e3831464a5057c519"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:17:35.185642"
+    }
+}

modules/nf-core/pairtools/parse/tests/nextflow.config

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

tests/config/pytest_modules.yml

@@ -983,9 +983,6 @@ oncocnv:
 paftools/sam2paf:
   - modules/nf-core/paftools/sam2paf/**
   - test/modules/nf-core/paftools/sam2paf/**
-pairtools/parse:
-  - modules/nf-core/pairtools/parse/**
-  - tests/modules/nf-core/pairtools/parse/**
 pairtools/restrict:
   - modules/nf-core/pairtools/restrict/**
   - tests/modules/nf-core/pairtools/restrict/**