Unit testing for COBALT

nf-core · Feb 4, 2025 · cb2a0f5 · cb2a0f5
1 parent c9a16b1
commit cb2a0f5
Showing 1 changed file with 90 additions and 0 deletions.
diff --git a/tests/modules/local/cobalt/main.nf.test b/tests/modules/local/cobalt/main.nf.test
@@ -0,0 +1,90 @@
+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("https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/reference_data/hmftools/5.34_38--2/dna_pipeline/copy_number/GC_profile.1000bp.38.cnp")
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.cobalt_ratio).exists() },
+                { assert path(process.out.cobalt_ratio).getText().contains("Chromosome\tPosition\tRatio") },
+                { assert path(process.out.cobalt_pcf).exists() },
+                { assert path(process.out.cobalt_pcf).getText().contains("Chromosome\tPosition\tRatio") },
+                { assert path(process.out.cobalt_gc).exists() },
+                { assert path(process.out.cobalt_gc).getText().contains("Chromosome\tPosition\tGCContent") }
+            )
+        }
+
+    }
+
+    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("https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/reference_data/hmftools/5.34_38--2/dna_pipeline/copy_number/GC_profile.1000bp.38.cnp")
+                input[2] = file("https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/reference_data/hmftools/5.34_38--2/dna_pipeline/copy_number/DiploidRegions.38.bed.gz")
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.cobalt_ratio).exists() },
+                { assert path(process.out.cobalt_ratio).getText().contains("Chromosome\tPosition\tRatio") },
+                { assert path(process.out.cobalt_pcf).exists() },
+                { assert path(process.out.cobalt_pcf).getText().contains("Chromosome\tPosition\tRatio") },
+                { assert path(process.out.cobalt_gc).exists() },
+                { assert path(process.out.cobalt_gc).getText().contains("Chromosome\tPosition\tGCContent") },
+                { assert path(process.out.cobalt_diploid_bed).exists() },
+                { assert path(process.out.cobalt_diploid_bed).getText().contains("chr\tstart\tend") }
+            )
+        }
+    }
+
+}