Add in content need for tests to pass on Azure (#27)

Closes #24

---------

Co-authored-by: Venkat Malladi <vmalladi@microsoft.com>

README.md

@@ -65,6 +65,10 @@ This process should succeed automatically with exit status 0.
 
 This process creates a file on the worker machine and then moves it to the working directory.
 
+### `TEST_CREATE_EMPTY_FILE`
+
+This process creates an empty file on the worker machine and then moves it to the working directory.
+
 ### `TEST_CREATE_FOLDER`
 
 This process creates a folder in the working directory.

main.nf

@@ -17,6 +17,19 @@ process TEST_CREATE_FILE {
     Creates a file on the worker node which is uploaded to the working directory.
     */
 
+    output:
+        path("*.txt"), emit: outfile
+
+    """
+    echo "test" > test.txt
+    """
+}
+
+process TEST_CREATE_EMPTY_FILE {
+    /*
+    Creates an empty file on the worker node which is uploaded to the working directory.
+    */
+
     output:
         path("*.txt"), emit: outfile
 
@@ -35,8 +48,8 @@ process TEST_CREATE_FOLDER {
 
     """
     mkdir -p test
-    touch test/test1.txt
-    touch test/test2.txt
+    echo "test1" > test/test1.txt
+    echo "test2" > test/test2.txt
     """
 }
 
@@ -240,7 +253,8 @@ workflow NF_CANARY {
         // Run tests
         TEST_SUCCESS()
         TEST_CREATE_FILE()
-        TEST_CREATE_FOLDER()
+        TEST_CREATE_EMPTY_FILE()
+	    TEST_CREATE_FOLDER()
         TEST_INPUT(test_file)
         TEST_BIN_SCRIPT()
         TEST_STAGE_REMOTE(remote_file)
@@ -258,6 +272,7 @@ workflow NF_CANARY {
             .mix(
                 TEST_SUCCESS.out,
                 TEST_CREATE_FILE.out,
+                TEST_CREATE_EMPTY_FILE.out,
                 TEST_CREATE_FOLDER.out,
                 TEST_INPUT.out,
                 TEST_BIN_SCRIPT.out,
@@ -278,4 +293,4 @@ workflow NF_CANARY {
 
 workflow {
     NF_CANARY()
-}
+}

tests/main.nf.test

@@ -15,8 +15,8 @@ nextflow_pipeline{
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.trace.tasks().size()     == 14 },
-                { assert workflow.trace.succeeded().size() == 13 },
+                { assert workflow.trace.tasks().size()     == 15 },
+                { assert workflow.trace.succeeded().size() == 14 },
                 { assert workflow.trace.failed().size()    == 1 },
                 { assert snapshot(workflow, path(params.outdir).list()).match() }
             )
@@ -37,8 +37,8 @@ nextflow_pipeline{
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.trace.tasks().size()     == 13 },
-                { assert workflow.trace.succeeded().size() == 12 },
+                { assert workflow.trace.tasks().size()     == 14 },
+                { assert workflow.trace.succeeded().size() == 13 },
                 { assert workflow.trace.failed().size()    == 1 },
                 { assert snapshot(workflow, path(params.outdir).list()).match() }
             )
@@ -81,8 +81,8 @@ nextflow_pipeline{
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.trace.tasks().size()     == 14 },
-                { assert workflow.trace.succeeded().size() == 13 },
+                { assert workflow.trace.tasks().size()     == 15 },
+                { assert workflow.trace.succeeded().size() == 14 },
                 { assert workflow.trace.failed().size()    == 1 },
                 { assert snapshot(workflow, path("${launchDir}/output").list()).match() }
             )

tests/main.nf.test.snap

@@ -14,8 +14,8 @@
                 "errorMessage": "",
                 "trace": {
                     "tasksFailed": 1,
-                    "tasksCount": 13,
-                    "tasksSucceeded": 12
+                    "tasksCount": 14,
+                    "tasksSucceeded": 13
                 },
                 "name": "workflow",
                 "success": true
@@ -32,7 +32,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-18T17:10:49.052904"
+        "timestamp": "2024-04-19T09:04:04.680628"
     },
     "Should publish to alternative directory": {
         "content": [
@@ -49,8 +49,8 @@
                 "errorMessage": "",
                 "trace": {
                     "tasksFailed": 1,
-                    "tasksCount": 14,
-                    "tasksSucceeded": 13
+                    "tasksCount": 15,
+                    "tasksSucceeded": 14
                 },
                 "name": "workflow",
                 "success": true
@@ -67,7 +67,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-18T17:10:53.086666"
+        "timestamp": "2024-04-19T09:04:08.847329"
     },
     "Should only run one process": {
         "content": [
@@ -115,8 +115,8 @@
                 "errorMessage": "",
                 "trace": {
                     "tasksFailed": 1,
-                    "tasksCount": 14,
-                    "tasksSucceeded": 13
+                    "tasksCount": 15,
+                    "tasksSucceeded": 14
                 },
                 "name": "workflow",
                 "success": true
@@ -133,6 +133,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-18T17:10:47.053474"
+        "timestamp": "2024-04-19T09:04:02.601858"
     }
 }

tests/main.test_create_empty_file.nf.test

@@ -0,0 +1,18 @@
+nextflow_process {
+
+    name "Test Process TEST_CREATE_EMPTY_FILE"
+    script "main.nf"
+    process "TEST_CREATE_EMPTY_FILE"
+
+    test("TEST_CREATE_EMPTY_FILE") {
+
+        then {
+            assertAll(                
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

tests/main.test_create_empty_file.nf.test.snap

@@ -0,0 +1,19 @@
+{
+    "TEST_CREATE_EMPTY_FILE": {
+        "content": [
+            {
+                "0": [
+                    "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "outfile": [
+                    "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T17:19:44.512229"
+    }
+}

tests/main.test_create_file.nf.test.snap

@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.txt:md5,d8e8fca2dc0f896fd7cb4cb0031ba249"
                 ],
                 "outfile": [
-                    "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.txt:md5,d8e8fca2dc0f896fd7cb4cb0031ba249"
                 ]
             }
         ],

tests/main.test_create_folder.nf.test.snap

@@ -4,14 +4,14 @@
             {
                 "0": [
                     [
-                        "test1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "test2.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test1.txt:md5,3e7705498e8be60520841409ebc69bc1",
+                        "test2.txt:md5,126a8a51b9d1bbd07fddc65819a542c3"
                     ]
                 ],
                 "outfolder": [
                     [
-                        "test1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "test2.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test1.txt:md5,3e7705498e8be60520841409ebc69bc1",
+                        "test2.txt:md5,126a8a51b9d1bbd07fddc65819a542c3"
                     ]
                 ]
             }