starting to add test

nextflow.config

@@ -94,13 +94,14 @@ params {
 }
 
 process {
-    queue = 'long-sl7,short-sl7'
+
+    // queue = 'long-sl7,short-sl7'
     cache = 'lenient'
     memory='4.5G'
     cpus='1'
     time='6h'
     scratch = false
-    containerOptions = { workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g)': null}
+    // containerOptions = { workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g)': null}
     container = 'perl:5.24-threaded-buster'
 
     withLabel: incr_time_cpus {
@@ -176,6 +177,17 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
     }
+    // Default configuration for test - Change accordingly
+    test {
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+    }
 
     // Original ExOrthist AWS Batch configuration
     // awsbatch {

nf-test.config

@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "test"
+
+}

tests/main.nf.test

@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test pipeline with default settings"
+    script "../main.nf"
+
+    test("Params: default") {
+
+        when {
+            params {
+                output = "$output"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+}

tests/nextflow.config

@@ -0,0 +1,27 @@
+
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+
+
+// Impose sensible resource limits for testing
+// process {
+//    withName: '.*' {
+//        cpus   = 2
+//        memory = 3.GB
+//        time   = 2.h
+//    }
+// }
+
+// Impose same minimum Nextflow version as the pipeline for testing
+manifest {
+    nextflowVersion = '!>=24.04.2'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }