Update nf-test to v0.8.2 (#91)

* update nf-test to v0.8.2
Should execute pipeline applying an additive model

* update .gitignore
Ignore .nf-test.log in commits

* update test case regenie_step2
add snapshot
remove redundant cases

* update snapshot regenie_step1

.github/workflows/ci-tests.yml

@@ -20,7 +20,7 @@ jobs:
     - name: Add nextflow to path
       run: echo "/opt/nextflow" >> $GITHUB_PATH;
     - name: Install nf-test
-      run: sudo bash; mkdir /opt/nf-test; cd /opt/nf-test; wget https://github.com/askimed/nf-test/releases/download/v0.8.0/nf-test-0.8.0.tar.gz; tar xvfz nf-test-*.tar.gz; chmod +x nf-test;
+      run: sudo bash; mkdir /opt/nf-test; cd /opt/nf-test; wget https://github.com/askimed/nf-test/releases/download/v0.8.2/nf-test-0.8.2.tar.gz; tar xvfz nf-test-*.tar.gz; chmod +x nf-test;
     - name: Add nf-test to pathdocker build -t genepi/nf-gwas .
       run: echo "/opt/nf-test" >> $GITHUB_PATH;
     - name: Run nf-test tests with development profile

.gitignore

@@ -8,3 +8,4 @@ tests/output
 nf-test
 .project
 .DS_Store
+.nf-test.log

tests/main.nf.test.snap

@@ -1,13 +1,13 @@
 {
     "Should execute pipeline applying an additive model": {
         "content": [
-            "Y1.regenie.gz:md5,e4ddf7505dc35e1173c4401f4090da76",
+            "Y1.regenie.gz:md5,3b46e913e302d59a27c87f989384a689",
             {
                 "tasksFailed": 0,
                 "tasksCount": 15,
                 "tasksSucceeded": 15
             }
         ],
-        "timestamp": "2023-09-08T15:21:44.585872"
+        "timestamp": "2023-12-14T13:41:14.112083"
     }
 }

tests/modules/local/regenie_step1.nf.test.snap

@@ -1,9 +1,9 @@
 {
     "Should execute regenie step 1 for 2 phenotypes ": {
         "content": [
-            "regenie_step1_out_1.loco.gz:md5,7acd8ecadafb0eb9bbab2eb8b529e54f",
-            "regenie_step1_out_2.loco.gz:md5,41ab9671090c2f7af3834242e691d18a"
+            "regenie_step1_out_1.loco.gz:md5,5e3f3bd230d519c0740ae158d2ba2f41",
+            "regenie_step1_out_2.loco.gz:md5,ff2327b54520a6885df85ad27cebcd19"
         ],
-        "timestamp": "2023-09-08T13:14:33.253877"
+        "timestamp": "2023-12-14T15:05:10.807967"
     }
 }

tests/modules/local/regenie_step2.nf.test

@@ -31,17 +31,13 @@ nextflow_process {
 
         then {
             assert process.success
-
             //check amount of processes
             assert process.trace.tasks().size() == 1
 
             with(process.out) {
+                assert snapshot(regenie_step2_out.get(0)).match()
                 with(regenie_step2_out.get(0)){
-                    assert size() == 3
-                    assert get(0) == "example"
-                    assert path(get(1)).md5 == 'd02411453e1236fb378020bb95246cc5'
-                    assert path(get(2)).md5 == '89086862ab0ea9b2a1a92f3bee0b55d3'
-
+
                     // access second element of first tuple
                     def lines = path(get(1)).readLinesGzip()
 

tests/modules/local/regenie_step2.nf.test.snap

@@ -0,0 +1,12 @@
+{
+    "Should execute regenie step2 without predictions": {
+        "content": [
+            [
+                "example",
+                "example.regenie.gz:md5,18c80204000d96c4cffbfd1859088111",
+                "example.regenie.Ydict:md5,89086862ab0ea9b2a1a92f3bee0b55d3"
+            ]
+        ],
+        "timestamp": "2023-12-14T14:47:08.826254"
+    }
+}