Additional tests for tumor-only mode

nf-core · Feb 4, 2025 · a8d5e94 · a8d5e94
1 parent 8552a82
commit a8d5e94
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Showing 2 changed files with 80 additions and 43 deletions.
diff --git a/tests/modules/local/amber/main.nf.test b/tests/modules/local/amber/main.nf.test
@@ -61,49 +61,41 @@ nextflow_process {
 
     }
 
-//     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] = []
-//                 """
-//             }
-//         }
+    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 {
-//             // assert process.success
-//             // assert snapshot(process.out).match()
-//             def amber_output_dir = process.out.amber_dir[0][1]
+        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("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() }
-//             )
-//         }
-//     }
+            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
@@ -56,6 +56,51 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-03T16:00:40.195219282"
+        "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"
     }
 }