Add nf-test for mergeBam module and merging workflow

tests/modules/mergeBam/sambamba/main.nf.test

@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process mergeBam"
+    script "modules/mergeBam/sambamba/main.nf"
+    process "mergeBam"
+
+    tag "module"
+
+    test("Should merge BAM files using sambamba") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+            }
+            process {
+                """
+                input[0] = Channel.from([
+                    [ "sample2", [ "test2", "test3" ], file("${baseDir}/data/test*/*.bam"), "bam", "GenomeAlignments", true]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

tests/modules/mergeBam/sambamba/main.nf.test.snap

@@ -0,0 +1,23 @@
+{
+    "Should merge BAM files using sambamba": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "sample2",
+                        "test2:test3",
+                        "sample2_m4_n10_toGenome.bam:md5,724ebe0d965d40decaa80c6b09e47ba5",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T11:08:00.400122"
+    }
+}

tests/modules/mergeBam/samtools/main.nf.test

@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process mergeBam"
+    script "modules/mergeBam/samtools/main.nf"
+    process "mergeBam"
+
+    tag "module"
+
+    test("Should merge BAM files using samtools") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+            }
+            process {
+                """
+                input[0] = Channel.from([
+                    [ "sample2", [ "test2", "test3" ], file("${baseDir}/data/test*/*.bam"), "bam", "GenomeAlignments", true]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

tests/modules/mergeBam/samtools/main.nf.test.snap

@@ -0,0 +1,23 @@
+{
+    "Should merge BAM files using samtools": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "sample2",
+                        "test2:test3",
+                        "sample2_m4_n10_toGenome.bam:md5,1aafe9aacc6e403ed8a5466a30549c85",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T11:27:59.686395"
+    }
+}

tests/workflows/merging.nf.test

@@ -0,0 +1,123 @@
+nextflow_workflow {
+
+    name "Test Workflow merging"
+    script "workflows/merging.nf"
+    workflow "merging"
+
+    tag "workflow"
+
+    test("Should merge genome BAM files using sambamba") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+                mergeBamTool = "sambamba"
+                markdupTool = "sambamba"
+            }
+            workflow {
+                """
+                input[0] = Channel.from([
+                    [ "sample2", "test2", file("${baseDir}/data/test2/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true],
+                    [ "sample2", "test3", file("${baseDir}/data/test3/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true]
+                ])
+                input[1] = Channel.empty()
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+    test("Should merge genome BAM files using samtools") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+                mergeBamTool = "samtools"
+                markdupTool = "sambamba"
+            }
+            workflow {
+                """
+                input[0] = Channel.from([
+                    [ "sample2", "test2", file("${baseDir}/data/test2/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true],
+                    [ "sample2", "test3", file("${baseDir}/data/test3/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true]
+                ])
+                input[1] = Channel.empty()
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+    test("Should merge all BAM files using samtools") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+                mergeBamTool = "samtools"
+                markdupTool = "sambamba"
+            }
+            workflow {
+                """
+                input[0] = Channel.from([
+                    [ "sample2", "test2", file("${baseDir}/data/test2/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true],
+                    [ "sample2", "test3", file("${baseDir}/data/test3/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true]
+                ])
+                input[1] = Channel.from([
+                    [ "sample2", "test2", file("${baseDir}/data/test2/sample2_m4_n10_toTranscriptome_sorted.bam"), "bam", "TranscriptomeAlignments", true],
+                    [ "sample2", "test3", file("${baseDir}/data/test3/sample2_m4_n10_toTranscriptome_sorted.bam"), "bam", "TranscriptomeAlignments", true]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+    test("Should merge all BAM files using sambamba") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+                mergeBamTool = "sambamba"
+                markdupTool = "sambamba"
+            }
+            workflow {
+                """
+                input[0] = Channel.from([
+                    [ "sample2", "test2", file("${baseDir}/data/test2/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true],
+                    [ "sample2", "test3", file("${baseDir}/data/test3/sample2_m4_n10_toGenome_sorted.bam"), "bam", "GenomeAlignments", true]
+                ])
+                input[1] = Channel.from([
+                    [ "sample2", "test2", file("${baseDir}/data/test2/sample2_m4_n10_toTranscriptome_sorted.bam"), "bam", "TranscriptomeAlignments", true],
+                    [ "sample2", "test3", file("${baseDir}/data/test3/sample2_m4_n10_toTranscriptome_sorted.bam"), "bam", "TranscriptomeAlignments", true]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+}