update tests organization

conf/test.config

@@ -25,8 +25,6 @@ params {
     validationSchemaIgnoreParams = 'genomes,igenomes_base,test_data'
 }
 
-includeConfig './test_data.config'
-
 process {
     withName: PRESEQ_LCEXTRAP {
         errorStrategy = 'ignore'

main.nf

@@ -28,7 +28,7 @@ params.bwameth_index = getGenomeAttribute('bwameth')
 */
 
 include { METHYLSEQ               } from './workflows/methylseq/methylseq'
-include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome/prepare_genome'
+include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome/'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
 

nf-test.config

@@ -3,14 +3,16 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir "/tmp"
-
-    // location of library folder that is added automatically to the classpath
-    libDir "tests/lib/"
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "nextflow.config"
+    configFile "tests/nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
-    profile ""
+    profile "test"
+
+    // load the necessary plugins
+    plugins {
+        load "[email protected]"
+    }
 }

subworkflows/local/bismark/tests/main.nf.test

@@ -0,0 +1,33 @@
+nextflow_workflow {
+
+    name "Test Workflow BISMARK"
+    script "../main.nf"
+    workflow "BISMARK"
+
+    test("Bismark Single-End") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = file("test-file.txt") // reads
+                input[1] = file("test-file.txt") // bismark_index
+                input[2] = file("test-file.txt") // skip_deduplication
+                input[3] = file("test-file.txt") // cytosine_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+}

subworkflows/local/bwameth/tests/main.nf.test

@@ -0,0 +1,34 @@
+nextflow_workflow {
+
+    name "Test Workflow BWAMETH"
+    script "subworkflows/local/bwameth/main.nf"
+    workflow "BWAMETH"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = file("test-file.txt") // reads
+                input[1] = file("test-file.txt") // bwameth_index
+                input[2] = file("test-file.txt") // fasta
+                input[3] = file("test-file.txt") // fasta_index
+                input[4] = file("test-file.txt") // skip_deduplication
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+}

subworkflows/local/prepare_genome/tests/main.nf.test

@@ -0,0 +1,33 @@
+nextflow_workflow {
+
+    name "Test Workflow PREPARE_GENOME"
+    script "subworkflows/local/prepare_genome/main.nf"
+    workflow "PREPARE_GENOME"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = file("test-file.txt") // fasta
+                input[1] = file("test-file.txt") // ch_fasta_index
+                input[2] = file("test-file.txt") // ch_bismark_index
+                input[3] = file("test-file.txt") // ch_bwameth_index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+}

tests/bismark.nf.test

@@ -0,0 +1,72 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+
+    test("Params: default") {
+
+        when {
+            params {
+                aligner        = "bismark"
+                save_reference = true
+                outdir         = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"),
+                            path("$outputDir/bismark/deduplicated/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam"),
+                            path("$outputDir/bismark/deduplicated/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam"),
+                            path("$outputDir/bismark/deduplicated/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam"),
+                            path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"),
+                            path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"),
+                            path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"),
+                            path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"),
+                            path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"),
+                            path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"),
+                            path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"),
+                            path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"),
+                            path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"),
+                            path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"),
+                            path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"),
+                            path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"),
+                            path("$outputDir/bismark/methylation_calls/methylation_calls/").list(),
+                            path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"),
+                            path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"),
+                            path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"),
+                            path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt"),
+                            path("$outputDir/bismark/reference_genome/BismarkIndex/").list(),
+                            path("$outputDir/qualimap/Ecoli/genome_results.txt"),
+                            path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"),
+                            path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"),
+                            path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
+                { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() },
+                { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() },
+                { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() },
+                { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() },
+                { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() },
+                { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() },
+                { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() },
+                { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() },
+                { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() },
+                { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() },
+                { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() },
+                { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() },
+                { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() },
+                { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() },
+                { assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() },
+                { assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() },
+                { assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() }
+            )
+        }
+
+    }
+
+}

tests/bismark_hisat.nf.test

@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}

tests/bwameth.nf.test

@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}

tests/nextflow.config

@@ -0,0 +1,38 @@
+/*
+========================================================================================
+    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/methylseq/2.7.0/'
+
+    fasta                        = "${params.pipelines_testdata_base_path}/reference/genome.fa"
+    fasta_index                  = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai"
+
+    validationSchemaIgnoreParams = 'genomes,igenomes_base,modules_testdata_base_path,pipelines_testdata_base_path'
+}
+
+// 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 }

workflows/methylseq/methylseq.nf

@@ -19,11 +19,11 @@ include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore
 
 // Aligner: bismark or bismark_hisat
 if( params.aligner =~ /bismark/ ){
-    include { BISMARK } from '../../subworkflows/local/bismark/bismark'
+    include { BISMARK } from '../../subworkflows/local/bismark/'
 }
 // Aligner: bwameth
 else if ( params.aligner == 'bwameth' ){
-    include { BWAMETH } from '../../subworkflows/local/bwameth/bwameth'
+    include { BWAMETH } from '../../subworkflows/local/bwameth/'
 }
 
 /*