nf-core · rhassaine · Jan 29, 2025 · Jan 29, 2025 · Jan 29, 2025 · Jan 31, 2025
diff --git a/.gitignore b/.gitignore
@@ -8,4 +8,5 @@ results/
 testing/
 testing*
 *.pyc
-null/
+.nf-test*
+.nf-test/
diff --git a/nf-test.config b/nf-test.config
@@ -0,0 +1,9 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "docker"
+    options "-dump-channels"
+
+}
diff --git a/tests/modules/local/amber/main.nf.test b/tests/modules/local/amber/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process AMBER"
+    script "modules/local/amber/main.nf"
+    process "AMBER"
+
+    test("AMBER testing tumor + normal") {
+
+        when {
+            params {
+                test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'
+            }
+            process {
+                """
+                // define inputs of the process here. Example:
+                // input[0] = file("test-file.txt")
+
+                input[0] = [
+                    [id: 'test',
+                    tumor_id: 'tumor_test',
+                    normal_id: 'normal_test'
+                    ],
+
+                    file(params.test_sample_data +  'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
+                    file(params.test_sample_data +  'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
+                    file(params.test_sample_data +  'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
+                    file(params.test_sample_data +  'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
+
+                ]
+
+                input[1] = 38 // ref_genome_version
+                input[2] = file("https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/reference_data/hmftools/5.34_38--2/dna_pipeline/copy_number/AmberGermlineSites.38.tsv.gz")
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // assert process.success
+            // assert snapshot(process.out).match()
+            def amber_output_dir = process.out.amber_dir[0][1]
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(amber_output_dir).resolve("amber.version").exists() },
+                { assert path(amber_output_dir).resolve("normal_test.amber.homozygousregion.tsv").exists() },
+                { assert path(amber_output_dir).resolve("normal_test.amber.snp.vcf.gz").exists() },
+                { assert path(amber_output_dir).resolve("normal_test.amber.snp.vcf.gz.tbi").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.baf.pcf").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.baf.tsv.gz").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.contamination.tsv").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.contamination.vcf.gz").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.contamination.vcf.gz.tbi").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.qc").exists() },
+                { assert path(process.out.versions[0]).exists() }
+            )
+        }
+
+    }
+
+    test("AMBER with tumor only") {
+        when {
+            params {
+                // publish_dir_mode = "symlink"
+                test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test', tumor_id: 'tumor_test'],
+                    file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
+                    [],
+                    file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = 38
+                input[2] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/AmberGermlineSites.38.tsv.gz")
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            def amber_output_dir = process.out.amber_dir[0][1]
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(amber_output_dir).resolve("amber.version").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.baf.pcf").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.baf.tsv.gz").exists() },
+                { assert path(amber_output_dir).resolve("tumor_test.amber.qc").exists() },
+                { assert path(process.out.versions[0]).exists() }
+            )
+        }
+    }
+
+}
diff --git a/tests/modules/local/amber/main.nf.test.snap b/tests/modules/local/amber/main.nf.test.snap
@@ -0,0 +1,106 @@
+{
+    "AMBER testing tumor + normal": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumor_test",
+                            "normal_id": "normal_test"
+                        },
+                        [
+                            "amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
+                            "normal_test.amber.homozygousregion.tsv:md5,d21abd62a26119eaf01ea8d1f66b9f05",
+                            "normal_test.amber.snp.vcf.gz:md5,44f59e7c11b3b348f647e0251732acc6",
+                            "normal_test.amber.snp.vcf.gz.tbi:md5,e4caffcadff308826156914dd6b43484",
+                            "tumor_test.amber.baf.pcf:md5,d4015414e9ccf00ab02c818a2a99a939",
+                            "tumor_test.amber.baf.tsv.gz:md5,7c6921d6c7742598b3e8b3f7fe8fea8d",
+                            "tumor_test.amber.contamination.tsv:md5,6fb3d29cc2c879b1db07cc8581a8fb70",
+                            "tumor_test.amber.contamination.vcf.gz:md5,5562d1e335c40ff733bbf751e37e541c",
+                            "tumor_test.amber.contamination.vcf.gz.tbi:md5,a359216fecd8b0a3eada28dc683300a1",
+                            "tumor_test.amber.qc:md5,9c502425aa5e1bf23569e1f60a32dcf1"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
+                ],
+                "amber_dir": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumor_test",
+                            "normal_id": "normal_test"
+                        },
+                        [
+                            "amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
+                            "normal_test.amber.homozygousregion.tsv:md5,d21abd62a26119eaf01ea8d1f66b9f05",
+                            "normal_test.amber.snp.vcf.gz:md5,44f59e7c11b3b348f647e0251732acc6",
+                            "normal_test.amber.snp.vcf.gz.tbi:md5,e4caffcadff308826156914dd6b43484",
+                            "tumor_test.amber.baf.pcf:md5,d4015414e9ccf00ab02c818a2a99a939",
+                            "tumor_test.amber.baf.tsv.gz:md5,7c6921d6c7742598b3e8b3f7fe8fea8d",
+                            "tumor_test.amber.contamination.tsv:md5,6fb3d29cc2c879b1db07cc8581a8fb70",
+                            "tumor_test.amber.contamination.vcf.gz:md5,5562d1e335c40ff733bbf751e37e541c",
+                            "tumor_test.amber.contamination.vcf.gz.tbi:md5,a359216fecd8b0a3eada28dc683300a1",
+                            "tumor_test.amber.qc:md5,9c502425aa5e1bf23569e1f60a32dcf1"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-04T08:41:54.940934927"
+    },
+    "AMBER with tumor only": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumor_test"
+                        },
+                        [
+                            "amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
+                            "tumor_test.amber.baf.pcf:md5,5b42f5fac4df8e88a1605943beda9eda",
+                            "tumor_test.amber.baf.tsv.gz:md5,938d30b5bd65598a4efc2b5c01f89ce1",
+                            "tumor_test.amber.qc:md5,9547e68ba672e08d6bd49e1e6f654ee8"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
+                ],
+                "amber_dir": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumor_test"
+                        },
+                        [
+                            "amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
+                            "tumor_test.amber.baf.pcf:md5,5b42f5fac4df8e88a1605943beda9eda",
+                            "tumor_test.amber.baf.tsv.gz:md5,938d30b5bd65598a4efc2b5c01f89ce1",
+                            "tumor_test.amber.qc:md5,9547e68ba672e08d6bd49e1e6f654ee8"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-04T08:42:14.429643438"
+    }
+}
diff --git a/tests/modules/local/cobalt/main.nf.test b/tests/modules/local/cobalt/main.nf.test
@@ -0,0 +1,88 @@
+nextflow_process {
+
+    name "Test Process COBALT"
+    script "modules/local/cobalt/main.nf"
+    process "COBALT"
+
+    test("COBALT testing tumor + normal") {
+
+        when {
+            params {
+                test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'// define parameters here. Example:
+            }
+            process {
+                """
+                // define inputs of the process here. Example:
+                // input[0] = file("test-file.txt")
+
+                input[0] = [
+                    [id: 'test',
+                    tumor_id: 'tumor_test',
+                    normal_id: 'normal_test'
+                    ],
+                    file(params.test_sample_data +  'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
+                    file(params.test_sample_data +  'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
+                    file(params.test_sample_data +  'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
+                    file(params.test_sample_data +  'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
+                ]
+                input[1] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/GC_profile.1000bp.38.cnp")
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            def cobalt_output_dir = process.out.cobalt_dir[0][1]
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(cobalt_output_dir).resolve("cobalt.version").exists() },
+                { assert path(cobalt_output_dir).resolve("tumor_test.cobalt.gc.median.tsv").exists() },
+                { assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.pcf").exists() },
+                { assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.tsv.gz").exists() },
+                { assert path(cobalt_output_dir).resolve("normal_test.cobalt.gc.median.tsv").exists() },
+                { assert path(cobalt_output_dir).resolve("normal_test.cobalt.ratio.median.tsv").exists() },
+                { assert path(cobalt_output_dir).resolve("normal_test.cobalt.ratio.pcf").exists() },
+                { assert path(process.out.versions[0]).exists() }
+            )
+        }
+
+    }
+
+    test("COBALT with tumor only") {
+        when {
+            params {
+                // publish_dir_mode = "symlink"
+                test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test', tumor_id: 'tumor_test'],
+                    file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
+                    [],
+                    file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/GC_profile.1000bp.38.cnp")
+                input[2] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/DiploidRegions.38.bed.gz")
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            def cobalt_output_dir = process.out.cobalt_dir[0][1]
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(cobalt_output_dir).resolve("cobalt.version").exists() },
+                { assert path(cobalt_output_dir).resolve("tumor_test.cobalt.gc.median.tsv").exists() },
+                { assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.pcf").exists() },
+                { assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.tsv.gz").exists() },
+                { assert path(process.out.versions[0]).exists() }
+    )
+}
+        }
+    }