nf-test side quest

mkdocs.yml

@@ -18,6 +18,8 @@ nav:
       - hello_nextflow/04_hello_modules.md
       - hello_nextflow/05_hello_containers.md
       - hello_nextflow/06_hello_config.md
+  - Side Quests:
+      - side_quests/nf-test.md
       - hello_nextflow/survey.md
       - hello_nextflow/next_steps.md
   - Nextflow for Genomics:
@@ -173,6 +175,7 @@ plugins:
         - basic_training/orientation.md
         - advanced/index.md
         - advanced/orientation.md
+        - side_quests/nf-test.md
   - i18n:
       docs_structure: suffix
       fallback_to_default: true

side-quests/nf-test/greetings.csv

@@ -0,0 +1,3 @@
+Hello
+Bonjour
+Holà

side-quests/nf-test/main.nf

@@ -0,0 +1,56 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Pipeline parameters
+ */
+params.input_file = "greetings.csv"
+
+/*
+ * Use echo to print 'Hello World!' to standard out
+ */
+process sayHello {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+        val greeting
+
+    output:
+        path "${greeting}-output.txt"
+
+    script:
+    """
+    echo '$greeting' > '$greeting-output.txt'
+    """
+}
+
+/*
+ * Use a text replace utility to convert the greeting to uppercase
+ */
+process convertToUpper {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+        path input_file
+
+    output:
+        path "UPPER-${input_file}"
+
+    script:
+    """
+    cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
+    """
+}
+
+workflow {
+
+    // create a channel for inputs from a CSV file
+    greeting_ch = Channel.fromPath(params.input_file).splitCsv().flatten()
+
+    // emit a greeting
+    sayHello(greeting_ch)
+
+    // convert the greeting to uppercase
+    convertToUpper(sayHello.out)
+}

side-quests/solutions/nf-test/tests/main.converttoupper.nf.test

@@ -0,0 +1,28 @@
+nextflow_process {
+
+    name "Test Process convertToUpper"
+    script "main.nf"
+    process "convertToUpper"
+
+    test("Should run without failures and produce correct output") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = "${projectDir}/greetings.csv"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

side-quests/solutions/nf-test/tests/main.converttoupper.nf.test.snap

@@ -0,0 +1,16 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "UPPER-greetings.csv:md5,f36624b0e040fa880e61fb1304b4b6b9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2025-02-19T11:57:20.215132756"
+    }
+}

side-quests/solutions/nf-test/tests/main.nf.test

@@ -0,0 +1,39 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                input_file = "${projectDir}/greetings.csv"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 6
+        }
+
+    }
+
+    test("Should produce correct output files") {
+
+        when {
+            params {
+                input_file = "${projectDir}/greetings.csv"
+            }
+        }
+
+        then {
+            assert file("$launchDir/results/Bonjour-output.txt").exists()
+            assert file("$launchDir/results/Hello-output.txt").exists()
+            assert file("$launchDir/results/Holà-output.txt").exists()
+            assert file("$launchDir/results/UPPER-Bonjour-output.txt").exists()
+            assert file("$launchDir/results/UPPER-Hello-output.txt").exists()
+            assert file("$launchDir/results/UPPER-Holà-output.txt").exists()
+        }
+
+    }
+}

side-quests/solutions/nf-test/tests/main.sayhello.nf.test

@@ -0,0 +1,26 @@
+nextflow_process {
+
+    name "Test Process sayHello"
+    script "main.nf"
+    process "sayHello"
+
+    test("Should run without failures and contain expected greeting") {
+        when {
+            params {
+                // define parameters here
+            }
+            process {
+                """
+                input[0] = "hello"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert path(process.out[0][0]).readLines().contains('hello')
+            assert !path(process.out[0][0]).readLines().contains('HELLO')
+        }
+    }
+
+}

side-quests/solutions/nf-test/tests/nextflow.config

@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/