Nf test

.gitignore

@@ -12,3 +12,6 @@ eggnog
 kofam
 kofamscan
 eukulele
+.nf-test.log
+nf-test
+.nf-test*

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#285](<[https://github.com/nf-core/metatdenovo/pull/285](https://github.com/nf-core/metatdenovo/pull/285)>) added nf-test for default settings.
 - [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module. Now the threshold for mapping a read to a contig is an identity of 0.9. The previous version of nf-core/metatdenovo used the default for BBMap, 0.76. This version might hence give slightly different results than the previous.
 - [#271](<[https://github.com/nf-core/metatdenovo/issues/271](https://github.com/nf-core/metatdenovo/issues/271)>) - Added flavor to SPADES modules
 

nf-test.config

@@ -0,0 +1,10 @@
+config {
+    // Location of nf-tests
+    testsDir "."
+
+    // nf-test directory used to create temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // Location of an optional nextflow.config file specific for executing pipeline tests
+    configFile "tests/nextflow.config"
+}

tests/main.nf.test

@@ -0,0 +1,39 @@
+nextflow_pipeline {
+    name "Test pipeline"
+    script "../main.nf"
+    tag "PIPELINE"
+
+    test("Run with profile test") {
+
+    when {
+        params {
+            outdir = "$outputDir"
+            input = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
+            skip_eukulele  = true
+            skip_eggnog    = true
+            skip_kofamscan = true
+        }
+    }
+
+    then {
+        assert workflow.success
+
+        assertAll(
+            { assert new File("$outputDir/trimgalore/SAMPLE1_PE_1.fastq.gz_trimming_report.txt").exists() },
+            { assert new File("$outputDir/trimgalore/fastqc/SAMPLE1_PE_1_val_1_fastqc.html").exists() },
+            { assert new File("$outputDir/megahit/megahit_out/megahit_assembly.log").exists() },
+            { assert new File("$outputDir/prodigal/megahit.prodigal.gff.gz").exists() },
+            { assert new File("$outputDir/samtools/SAMPLE1_PE.sorted.bam.bai").exists() },
+            { assert new File("$outputDir/bbmap/logs/SAMPLE1_PE.bbmap.log").exists() },
+            { assert new File("$outputDir/featurecounts/SAMPLE1_PE.featureCounts.txt.summary").exists() },
+            { assert new File("$outputDir/summary_tables/megahit.prodigal.counts.tsv.gz").exists() },
+            { assert new File("$outputDir/summary_tables/megahit.prodigal.overall_stats.tsv.gz").exists() },
+            { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
+            { assert new File("$outputDir/pipeline_info/nf_core_metatdenovo_software_mqc_versions.yml").exists() }
+            { assert snapshot(
+                path("${params.outdir}/trimgalore/SAMPLE1_PE_1.fastq.gz_trimming_report.txt"))
+                .match("output_files")
+            }
+        )
+    }
+}

tests/main.nf.test.snap

@@ -0,0 +1,12 @@
+{
+    "output_files": {
+        "content": [
+            "SAMPLE1_PE_1.fastq.gz_trimming_report.txt:md5,9c4b1b4309830cba58fc4a298ab4431e"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-22T11:15:50.396953549"
+    }
+}

tests/nextflow.config

@@ -0,0 +1,33 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+
+params {
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+
+    // Base directory for nf-core/rnaseq test data
+    pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/'
+}
+
+// Impose sensible resource limits for testing
+process {
+    withName: '.*' {
+        cpus   = 4
+        memory = 4.GB
+        time   = 2.h
+    }
+}
+
+// Impose same minimum Nextflow version as the pipeline for testing
+manifest {
+    nextflowVersion = '!>=23.04.0'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }