port bam split by region to nf-test

subworkflows/nf-core/bam_split_by_region/tests/main.nf.test

@@ -0,0 +1,45 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core subworkflows test bam_split_by_region
+nextflow_workflow {
+
+    name "Test Subworkflow BAM_SPLIT_BY_REGION"
+    script "../main.nf"
+    workflow "BAM_SPLIT_BY_REGION"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/bam_split_by_region"
+    tag "samtools"
+    tag "samtools/sort"
+    tag "samtools/index"
+
+    config "./nextflow.config"
+
+    test("homo_sapiens - test_paired_end_markduplicates_sorted_bam") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id: 'test', single_end: false ],
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.bam_bai.findAll { file(it.get(1)).name }.toSorted(),
+                    workflow.out.bam_bai.findAll { bam(it.get(1)).getReadsMD5() }.toSorted(),
+                    workflow.out.bam_bai.findAll { file(it.get(2)).name }.toSorted(),
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+}

subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap

@@ -0,0 +1,102 @@
+{
+    "homo_sapiens - test_paired_end_markduplicates_sorted_bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:24132499-24910998"
+                    },
+                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
+                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:25689497-46709983"
+                    },
+                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
+                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:1-23354000"
+                    },
+                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
+                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:24132499-24910998"
+                    },
+                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
+                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:25689497-46709983"
+                    },
+                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
+                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:1-23354000"
+                    },
+                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
+                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:24132499-24910998"
+                    },
+                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
+                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:25689497-46709983"
+                    },
+                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
+                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:1-23354000"
+                    },
+                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
+                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
+                ]
+            ],
+            [
+                "versions.yml:md5,022ce36c7637b4c28f9e7a3b6d788543",
+                "versions.yml:md5,1430b8967dea6b0eb5a65313c8d81e81"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T08:59:50.32521715"
+    }
+}

subworkflows/nf-core/bam_split_by_region/tests/nextflow.config

@@ -0,0 +1,6 @@
+process {
+    withName: "BAM_SPLIT_BY_REGION:SAMTOOLS_VIEW" {
+        ext.args2 = { "${meta.genomic_region}" } // Specifies the chromosome name used for splitting the input bam file.
+        ext.prefix = { "${meta.id}_${meta.genomic_region}" }
+    }
+}

tests/config/pytest_modules.yml

@@ -426,9 +426,6 @@ subworkflows/bam_markduplicates_samtools:
 subworkflows/bam_ngscheckmate:
   - subworkflows/nf-core/bam_ngscheckmate/**
   - tests/subworkflows/nf-core/bam_ngscheckmate/**
-subworkflows/bam_split_by_region:
-  - subworkflows/nf-core/bam_split_by_region/**
-  - tests/subworkflows/nf-core/bam_split_by_region/**
 subworkflows/bam_tumor_normal_somatic_variant_calling_gatk:
   - subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**
   - tests/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**