Merge pull request nf-core#1220 from adamrtalbot/nf-test-init

nf-test at the pipeline level

.gitignore

@@ -1,8 +1,12 @@
+*.pyc
+.DS_Store
 .nextflow*
-work/
+.nf-test.log
 data/
+nf-test
+.nf-test*
 results/
-.DS_Store
-testing/
+test.xml
 testing*
-*.pyc
+testing/
+work/

.nf-core.yml

@@ -3,6 +3,7 @@ lint:
   files_unchanged:
     - assets/email_template.html
     - assets/email_template.txt
+    - .gitignore
   files_exist:
     - conf/modules.config
   nextflow_config:

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats
 - [PR #1216](https://github.com/nf-core/rnaseq/pull/1216) - Delocalise catadditionalfasta ([#1162](https://github.com/nf-core/rnaseq/issues/1162))
 - [PR #1218](https://github.com/nf-core/rnaseq/pull/1218) - Template update for nf-core/tools v2.13
+- [PR #1220](https://github.com/nf-core/rnaseq/pull/1220) - Initialise nf-test and add pipeline level test
 
 ### Parameters
 

nf-test.config

@@ -0,0 +1,12 @@
+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"
+
+    profile "test"
+}

tests/lib/UTILS.groovy

@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from software_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}

tests/main.nf.test

@@ -0,0 +1,39 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "rnaseq"
+    tag "PIPELINE"
+
+    test("Run with profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
+            }
+        }
+
+        then {
+            assert workflow.success
+
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
+                { assert snapshot(path("$outputDir/bbsplit/").list(),
+                    path("$outputDir/salmon/").list(),
+                    path("$outputDir/star_salmon/").list(),
+                    path("$outputDir/trimgalore/").list()) },
+                { assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_1_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_2_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP1_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP2_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/WT_REP1_1_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/WT_REP1_2_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/WT_REP2_1_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/WT_REP2_2_fastqc.html").exists() },
+                { assert new File("$outputDir/multiqc/star_salmon/multiqc_report.html").exists() }
+            )
+        }
+    }
+}

tests/main.nf.test.snap

@@ -0,0 +1,12 @@
+{
+    "single_end_software_versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, CAT_ADDITIONAL_FASTA={python=3.9.5}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DESEQ2_QC_PSEUDO={bioconductor-deseq2=1.28.0, r-base=4.0.3}, DESEQ2_QC_STAR_SALMON={bioconductor-deseq2=1.28.0, r-base=4.0.3}, DUPRADAR={bioconductor-dupradar=1.28.0, r-base=4.2.1}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.10}, GUNZIP_GTF={gunzip=1.10}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.0.0}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SE_GENE={bioconductor-summarizedexperiment=1.24.0, r-base=4.1.1}, STAR_ALIGN={gawk=5.1.0, samtools=1.16.1, star=2.7.9a}, STAR_GENOMEGENERATE={gawk=5.1.0, samtools=1.16.1, star=2.7.9a}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, TX2GENE={python=3.9.5}, TXIMPORT={bioconductor-tximeta=1.12.0, r-base=4.1.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.30}, Workflow={nf-core/rnaseq=3.15.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-09T16:13:24.846838"
+    }
+}

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   = 2
+        memory = 3.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 }