Added nf-test for biobambam/bamsormadup (#6579)

modules/nf-core/biobambam/bamsormadup/main.nf

@@ -48,4 +48,22 @@ process BIOBAMBAM_BAMSORMADUP {
         bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
+    if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."
+
+    """
+    touch ${prefix}.${suffix}
+    touch ${prefix}.metrics.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamcat: \$(echo \$(bamcat --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
+        bamcollate2: \$(echo \$(bamcollate2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
+        bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
+    END_VERSIONS
+    """
 }

modules/nf-core/biobambam/bamsormadup/tests/main.nf.test

@@ -0,0 +1,105 @@
+
+nextflow_process {
+
+    name "Test Process BIOBAMBAM_BAMSORMADUP"
+    script "../main.nf"
+    process "BIOBAMBAM_BAMSORMADUP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "biobambam"
+    tag "biobambam/bamsormadup"
+
+    test("test-biobambam-bamsormadup-multi-input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+				]
+				input[1] = [[:],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.bam_index,
+					process.out.cram,
+					file(process.out.metrics[0][1]).readLines()[3..5],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-biobambam-bamsormadup-single-input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                    ]
+				]
+				input[1] = [[:],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.bam_index,
+					process.out.cram,
+					file(process.out.metrics[0][1]).readLines()[3..5],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-biobambam-bamsormadup-single-input-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                    ]
+				]
+				input[1] = [[:],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/biobambam/bamsormadup/tests/main.nf.test.snap

@@ -0,0 +1,115 @@
+{
+    "test-biobambam-bamsormadup-single-input": {
+        "content": [
+            "e296148e4f68882cc91fb624e392f539",
+            [
+
+            ],
+            [
+
+            ],
+            [
+                "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE",
+                "lib1\t3\t97\t3\t0\t0\t0\t0\t-1",
+                ""
+            ],
+            [
+                "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T22:00:39.772883"
+    },
+    "test-biobambam-bamsormadup-multi-input": {
+        "content": [
+            "3dc03384b330e3f16e15691c9189e890",
+            [
+
+            ],
+            [
+
+            ],
+            [
+                "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE",
+                "lib1\t3\t97\t3\t0\t0\t0\t0\t-1",
+                "testN\t0\t2820\t2\t0\t828\t0\t0.293617\t3807"
+            ],
+            [
+                "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T22:00:31.187999"
+    },
+    "test-biobambam-bamsormadup-single-input-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_index": [
+
+                ],
+                "cram": [
+
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:57:13.430982"
+    }
+}

tests/config/pytest_modules.yml

@@ -52,9 +52,6 @@ bedtools/intersect:
 bedtools/unionbedg:
   - modules/nf-core/bedtools/unionbedg/**
   - tests/modules/nf-core/bedtools/unionbedg/**
-biobambam/bamsormadup:
-  - modules/nf-core/biobambam/bamsormadup/**
-  - tests/modules/nf-core/biobambam/bamsormadup/**
 biohansel:
   - modules/nf-core/biohansel/**
   - tests/modules/nf-core/biohansel/**