Add test to verify no vcf/vcf_index output

Author: bagnacan

modules/nf-core/paraphase/tests/main.nf.test

@@ -100,6 +100,43 @@ nextflow_process {
         }
     }
 
+    test("homo_sapiens - [ bam, bai ], no_vcf") {
+
+        config "./nextflow.no_vcf.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                ]
+                input[1] = TABIX_BGZIP.out.output
+                input[2] = [
+                    [ id:'test_config' ],
+                    file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.vcf?.isEmpty() },
+                { assert process.out.vcf_index?.isEmpty() },
+                { assert snapshot(
+                    file(process.out.json.get(0).get(1)).readLines()[0..28],
+                    bam(process.out.bam.get(0).get(1)).getReadsMD5(),
+                    file(process.out.bai.get(0).get(1)).name,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
     test("homo_sapiens - [ bam, bai ], config - csi_index") {
 
         config "./nextflow.csi_index.config"