Merge branch 'main' into main

seqeralabs · Apr 18, 2024 · 3a78da3 · 3a78da3
2 parents 2fb3aff + 3d0d980
commit 3a78da3
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Showing 28 changed files with 221 additions and 99 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -8,8 +8,8 @@
                 "esbenp.prettier-vscode",
                 "redhat.vscode-yaml",
                 "GitHub.vscode-pull-request-github",
-                "github.vscode-github-actions",
-            ],
-        },
-    },
+                "github.vscode-github-actions"
+            ]
+        }
+    }
 }
diff --git a/README.md b/README.md
@@ -117,6 +117,6 @@ Tests moving a file within the working directory.
 
 Tests moving the contents of a folder to a new folder within the working directory.
 
-```
+### `TEST_VAL_INPUT`
 
-```
+Test a process can accept a value as input.
diff --git a/main.nf b/main.nf
@@ -195,6 +195,37 @@ process TEST_MV_FOLDER_CONTENTS {
     """
 }
 
+process TEST_STDOUT {
+    /*
+    This process should create and capture STDOUT
+    */
+
+    output:
+        stdout
+
+    script:
+    """
+    """
+}
+
+process TEST_VAL_INPUT {
+    /*
+    This process should read in val and echo to STDOUT
+    */
+
+
+    input:
+        val input
+
+    output:
+        stdout
+
+    script:
+    """
+    echo $input
+    """
+}
+
 workflow NF_CANARY {
 
     main:
@@ -220,7 +251,8 @@ workflow NF_CANARY {
         TEST_IGNORED_FAIL()
         TEST_MV_FILE()
         TEST_MV_FOLDER_CONTENTS()
-
+        TEST_VAL_INPUT("Hello World")
+
         // POC of emitting the channel
         Channel.empty()
             .mix(

diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -13,11 +13,13 @@ nextflow_pipeline{
         }
 
         then {
-            assert workflow.success
-            assert workflow.trace.tasks().size()     == 13
-            assert workflow.trace.succeeded().size() == 12
-            assert workflow.trace.failed().size()    == 1
-            assert snapshot(workflow, path(params.outdir).list()).match()
+            assertAll(
+                { assert workflow.success },
+                { 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() }
+            )
         }
 
     }
@@ -33,11 +35,13 @@ nextflow_pipeline{
         }
 
         then {
-            assert workflow.success
-            assert workflow.trace.tasks().size()     == 12
-            assert workflow.trace.succeeded().size() == 11
-            assert workflow.trace.failed().size()    == 1
-            assert snapshot(workflow, path(params.outdir).list()).match()
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.trace.tasks().size()     == 13 },
+                { assert workflow.trace.succeeded().size() == 12 },
+                { assert workflow.trace.failed().size()    == 1 },
+                { assert snapshot(workflow, path(params.outdir).list()).match() }
+            )
         }
 
     }
@@ -54,11 +58,13 @@ nextflow_pipeline{
         }
 
         then {
-            assert workflow.success
-            assert workflow.trace.tasks().size()     == 1
-            assert workflow.trace.succeeded().size() == 1
-            assert workflow.trace.failed().size()    == 0
-            assert snapshot(workflow, path(params.outdir).list()).match()
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.trace.tasks().size()     == 1 },
+                { assert workflow.trace.succeeded().size() == 1 },
+                { assert workflow.trace.failed().size()    == 0 },
+                { assert snapshot(workflow, path(params.outdir).list()).match() }
+            )
         }
 
     }
@@ -73,11 +79,13 @@ nextflow_pipeline{
         }
 
         then {
-            assert workflow.success
-            assert workflow.trace.tasks().size()     == 13
-            assert workflow.trace.succeeded().size() == 12
-            assert workflow.trace.failed().size()    == 1
-            assert snapshot(workflow, path("${launchDir}/output").list()).match()
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.trace.tasks().size()     == 14 },
+                { assert workflow.trace.succeeded().size() == 13 },
+                { assert workflow.trace.failed().size()    == 1 },
+                { assert snapshot(workflow, path("${launchDir}/output").list()).match() }
+            )
         }
 
     }

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
@@ -14,8 +14,8 @@
                 "errorMessage": "",
                 "trace": {
                     "tasksFailed": 1,
-                    "tasksCount": 12,
-                    "tasksSucceeded": 11
+                    "tasksCount": 13,
+                    "tasksSucceeded": 12
                 },
                 "name": "workflow",
                 "success": true
@@ -28,7 +28,11 @@
                 "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2023-10-04T12:09:12.963778"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T17:10:49.052904"
     },
     "Should publish to alternative directory": {
         "content": [
@@ -45,8 +49,8 @@
                 "errorMessage": "",
                 "trace": {
                     "tasksFailed": 1,
-                    "tasksCount": 13,
-                    "tasksSucceeded": 12
+                    "tasksCount": 14,
+                    "tasksSucceeded": 13
                 },
                 "name": "workflow",
                 "success": true
@@ -59,7 +63,11 @@
                 "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2023-10-04T12:20:22.461185"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T17:10:53.086666"
     },
     "Should only run one process": {
         "content": [
@@ -86,6 +94,10 @@
 
             ]
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
         "timestamp": "2023-10-04T12:17:23.982939"
     },
     "Should run without failures": {
@@ -103,8 +115,8 @@
                 "errorMessage": "",
                 "trace": {
                     "tasksFailed": 1,
-                    "tasksCount": 13,
-                    "tasksSucceeded": 12
+                    "tasksCount": 14,
+                    "tasksSucceeded": 13
                 },
                 "name": "workflow",
                 "success": true
@@ -117,6 +129,10 @@
                 "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2023-10-04T12:07:58.679961"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T17:10:47.053474"
     }
 }
diff --git a/tests/main.test_bin_script.test b/tests/main.test_bin_script.test
@@ -4,11 +4,13 @@ nextflow_process {
     script "main.nf"
     process "TEST_BIN_SCRIPT"
 
-    test("Should run without failures") {
+    test("TEST_BIN_SCRIPT") {
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
         }
 
     }

diff --git a/tests/main.test_create_file.nf.test b/tests/main.test_create_file.nf.test
@@ -4,11 +4,13 @@ nextflow_process {
     script "main.nf"
     process "TEST_CREATE_FILE"
 
-    test("Should run without failures") {
+    test("TEST_CREATE_FILE") {
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll(                
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
         }
 
     }

diff --git a/tests/main.test_create_file.nf.test.snap b/tests/main.test_create_file.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Should run without failures": {
+    "TEST_CREATE_FILE": {
         "content": [
             {
                 "0": [
@@ -10,6 +10,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-04T11:56:41.550158"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T17:19:44.512229"
     }
 }
diff --git a/tests/main.test_create_folder.nf.test b/tests/main.test_create_folder.nf.test
@@ -4,11 +4,13 @@ nextflow_process {
     script "main.nf"
     process "TEST_CREATE_FOLDER"
 
-    test("Should run without failures") {
+    test("TEST_CREATE_FOLDER") {
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
         }
 
     }

diff --git a/tests/main.test_create_folder.nf.test.snap b/tests/main.test_create_folder.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Should run without failures": {
+    "TEST_CREATE_FOLDER": {
         "content": [
             {
                 "0": [
@@ -16,6 +16,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-04T11:56:39.696681"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T17:19:42.631931"
     }
 }
diff --git a/tests/main.test_ignore_fail.test b/tests/main.test_ignore_fail.test
@@ -4,13 +4,15 @@ nextflow_process {
     script "main.nf"
     process "TEST_IGNORED_FAIL"
 
-    test("Should run without failures") {
+    test("TEST_IGNORED_FAIL") {
 
         then {
-            assert process.success
-            assert snapshot(process).match()
-            assert process.trace.failed().size() == 1
-            assert process.trace.succeeded().size() == 0
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process).match() },
+                { assert process.trace.failed().size() == 1 },
+                { assert process.trace.succeeded().size() == 0 }
+            )
         }
 
     }

diff --git a/tests/main.test_input.nf.test b/tests/main.test_input.nf.test
@@ -4,7 +4,7 @@ nextflow_process {
     script "main.nf"
     process "TEST_INPUT"
 
-    test("Should run without failures") {
+    test("TEST_INPUT") {
 
         when {
             process {
@@ -15,8 +15,10 @@ nextflow_process {
         }
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
         }
 
     }

diff --git a/tests/main.test_input.nf.test.snap b/tests/main.test_input.nf.test.snap
@@ -1,12 +1,16 @@
 {
-    "Should run without failures": {
+    "TEST_INPUT": {
         "content": [
             {
                 "0": [
                     "alpha\n"
                 ]
             }
         ],
-        "timestamp": "2023-10-04T11:56:21.166077"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T17:19:23.807701"
     }
 }
diff --git a/tests/main.test_mv_file.nf.test b/tests/main.test_mv_file.nf.test
@@ -4,11 +4,13 @@ nextflow_process {
     script "main.nf"
     process "TEST_MV_FILE"
 
-    test("Should run without failures") {
+    test("TEST_MV_FILE") {
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
         }
 
     }