Add snapshots to qc test

tests/main.nf.test

@@ -39,35 +39,18 @@ nextflow_pipeline {
             def quality_control_log = file("${outputDir}/cloudgene.report.json")
             assert quality_control_log.exists()
             assert quality_control_log.text.contains("Remaining sites in total: 7,735")
-
-        }
-
-    }
 
-    test("Should run QC-only and check statistic files") {
-
-        when {
-            params {
-                project  = "test-job"
-                build = "hg19"
-                files = "$projectDir/tests/data/input/chr20-phased/*.vcf.gz"
-                population = "eur"
-                mode = "qc-only"
-                refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2/cloudgene.yaml"
-                output = "${outputDir}"
-            }
-        }
-
-        then {
-            assert workflow.success
-
-            def quality_control_log = file("${outputDir}/cloudgene.report.json")
-            assert quality_control_log.exists()
-            assert quality_control_log.text.contains("Remaining sites in total: 7,735")
             def typed_file = file("${outputDir}/statistics/typed-only.txt")
             assert typed_file.exists()
+
             def snps_file = file("${outputDir}/statistics/snps-excluded.txt")
-            assert snps_file.exists()
+            assert snps_file.exists()            
+
+            assert snapshot(
+                quality_control_log.text,
+                typed_file.text,
+                snps_file.text
+            ).match()
 
         }
 
@@ -282,6 +265,7 @@ nextflow_pipeline {
             def quality_control_log = file("${outputDir}/cloudgene.report.json")
             assert quality_control_log.exists()
             assert quality_control_log.text.contains("Remaining sites in total: 7,735")
+            assert snapshot(quality_control_log.text).match()
 
 
             def imputed_chr_20 = file("${outputDir}/chr_20.zip");

tests/main.nf.test.snap

@@ -0,0 +1,24 @@
+{
+    "Should run with eagle and without encryption and compression": {
+        "content": [
+            "[{\"command\":\"LOG\",\"params\":[\"Reference Panel Ranges: genome-wide\"]},{\"command\":\"BEGIN_TASK\",\"params\":[\"Running Calculating QC Statistics...\"]},{\"command\":\"UPDATE_TASK\",\"params\":[\"Calculating QC Statistics [1/1]\\n\\nAnalyze file chr20.R50.merged.1.330k.recode.small.vcf.gz...\",3]},{\"command\":\"END_TASK\",\"params\":[\"Calculating QC Statistics\",0]},{\"command\":\"MESSAGE\",\"params\":[\"\\u003cb\\u003eStatistics:\\u003c/b\\u003e \\nAlternative allele frequency \\u003e 0.5 sites: 2,296\\nReference Overlap: 99.00 %\\nMatch: 7,735\\nAllele switch: 0\\nStrand flip: 0\\nStrand flip and allele switch: 0\\nA/T, C/G genotypes: 0\\n\\u003cb\\u003eFiltered sites:\\u003c/b\\u003e \\nFilter flag set: 0\\nInvalid alleles: 0\\nMultiallelic sites: 0\\nDuplicated sites: 0\\nNonSNP sites: 0\\nMonomorphic sites: 11\\nAllele mismatch: 0\\nSNPs call rate \\u003c 90%: 0\",0]},{\"command\":\"MESSAGE\",\"params\":[\"Excluded sites in total: 11\\nRemaining sites in total: 7,735\\nSee snps-excluded.txt for details\\nTyped only sites: 78\\nSee typed-only.txt for details\\n\",2]}]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-06-15T14:38:57.145373"
+    },
+    "Should run QC-only": {
+        "content": [
+            "[{\"command\":\"LOG\",\"params\":[\"Reference Panel Ranges: genome-wide\"]},{\"command\":\"BEGIN_TASK\",\"params\":[\"Running Calculating QC Statistics...\"]},{\"command\":\"UPDATE_TASK\",\"params\":[\"Calculating QC Statistics [1/1]\\n\\nAnalyze file chr20.R50.merged.1.330k.recode.small.vcf.gz...\",3]},{\"command\":\"END_TASK\",\"params\":[\"Calculating QC Statistics\",0]},{\"command\":\"MESSAGE\",\"params\":[\"\\u003cb\\u003eStatistics:\\u003c/b\\u003e \\nAlternative allele frequency \\u003e 0.5 sites: 2,296\\nReference Overlap: 99.00 %\\nMatch: 7,735\\nAllele switch: 0\\nStrand flip: 0\\nStrand flip and allele switch: 0\\nA/T, C/G genotypes: 0\\n\\u003cb\\u003eFiltered sites:\\u003c/b\\u003e \\nFilter flag set: 0\\nInvalid alleles: 0\\nMultiallelic sites: 0\\nDuplicated sites: 0\\nNonSNP sites: 0\\nMonomorphic sites: 11\\nAllele mismatch: 0\\nSNPs call rate \\u003c 90%: 0\",0]},{\"command\":\"MESSAGE\",\"params\":[\"Excluded sites in total: 11\\nRemaining sites in total: 7,735\\nSee snps-excluded.txt for details\\nTyped only sites: 78\\nSee typed-only.txt for details\\n\",2]}]",
+            "#Position\n20:161502:C:T\n20:775376:T:G\n20:775842:C:T\n20:1438230:C:T\n20:2638579:T:C\n20:3193842:C:A\n20:3580168:G:A\n20:3811433:T:C\n20:4063862:A:G\n20:4578080:G:A\n20:7541572:A:G\n20:7581461:T:G\n20:7928922:A:G\n20:8364799:G:T\n20:10243251:T:C\n20:11005238:A:C\n20:12173825:T:C\n20:13290738:T:C\n20:13582476:A:C\n20:13650883:T:G\n20:13929943:C:T\n20:13998098:G:A\n20:14794361:A:G\n20:14921606:G:A\n20:16066764:G:A\n20:16070941:C:T\n20:16116624:G:A\n20:16120763:A:G\n20:17596155:C:A\n20:17600357:G:A\n20:17845755:T:C\n20:18284404:C:T\n20:18389203:T:C\n20:19025636:C:T\n20:20130511:T:C\n20:20516020:T:C\n20:21628586:C:T\n20:21863397:A:G\n20:21939656:C:T\n20:23682810:A:G\n20:23725019:A:G\n20:24261606:T:C\n20:24691928:T:G\n20:24955981:T:C\n20:25136824:A:G\n20:25948327:A:G\n20:26307797:T:C\n20:31590686:C:A\n20:35673056:C:T\n20:39048873:A:C\n20:39792063:A:G\n20:40093956:A:C\n20:40387411:T:C\n20:40706295:T:C\n20:43506247:G:A\n20:43668473:G:A\n20:44011546:C:T\n20:46332216:T:C\n20:46435339:T:C\n20:47263751:T:C\n20:47479776:C:T\n20:48143362:T:C\n20:48403371:T:C\n20:50395283:T:C\n20:50475418:G:A\n20:53251910:G:A\n20:53515863:C:A\n20:54264333:C:T\n20:54692704:A:G\n20:54961463:T:C\n20:56637477:A:G\n20:57304273:C:T\n20:58098827:G:A\n20:58114167:T:C\n20:59121456:A:G\n20:61381218:G:A\n20:61644330:A:G\n20:61706750:C:T",
+            "#Position\tFilterType\t Info\n20:2187430:G:A\tMonomorphic\n20:24404652:C:T\tMonomorphic\n20:24424220:C:T\tMonomorphic\n20:25282967:C:T\tMonomorphic\n20:39005139:C:T\tMonomorphic\n20:45867852:A:G\tMonomorphic\n20:45873923:C:T\tMonomorphic\n20:48575315:C:T\tMonomorphic\n20:52269701:C:A\tMonomorphic\n20:54179856:G:T\tMonomorphic\n20:59363320:G:A\tMonomorphic"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-06-15T15:37:22.79833"
+    }
+}