test: Add full test

assets/nf-test_full.config

@@ -0,0 +1,38 @@
+config {
+    // location for all nf-test tests
+    testsDir = "."
+
+    // nf-test directory including temporary files for each test
+    workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile = "assets/oncoflow_test_full.config"
+
+    // ignore tests coming from the nf-core/modules repo
+    ignore = [
+        'modules/nf-core/**/tests/*',
+        'subworkflows/nf-core/**/tests/*',
+    ]
+
+    // run all test with defined profile(s) from the main nextflow.config
+    profile = "test_full"
+
+    // list of filenames or patterns that should be trigger a full test run
+    triggers = [
+        '.github/actions/nf-test/action.yml',
+        '.github/workflows/nf-test.yml',
+        'assets/schema_input.json',
+        'bin/*',
+        'conf/test.config',
+        'nextflow.config',
+        'nextflow_schema.json',
+        'nf-test.config',
+        'tests/.nftignore',
+        'tests/nextflow.config',
+    ]
+
+    // load the necessary plugins
+    plugins {
+        load "nft-utils@0.0.3"
+    }
+}

assets/oncoflow_test_full.config

@@ -0,0 +1,79 @@
+// General pipeline parameters that should be the same for all oncorefiner cases
+params {
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/Clinical-Genomics/test-datasets/61dce843b868caaee4135d33509af38aaa80724b/'
+
+    fasta               = params.pipelines_testdata_base_path + 'reference/GRCh38/GRCh38_masked_exclusions_alts_hlas_subset.fasta'
+    fai                 = params.pipelines_testdata_base_path + 'reference/GRCh38/GRCh38_masked_exclusions_alts_hlas_subset.fasta.fai'
+
+    vep_cache           = params.pipelines_testdata_base_path + 'reference/GRCh38/vep_cache.tar.gz'
+    vep_plugin_files    = params.pipelines_testdata_base_path + 'reference/GRCh38/vep_files.csv'
+
+    vcfanno_toml        = params.pipelines_testdata_base_path + 'reference/GRCh38/grch38_vcfanno_config.toml'
+    vcfanno_resources   = params.pipelines_testdata_base_path + 'reference/GRCh38/grch38_vcfanno_resources.txt'
+    vcfanno_lua         = params.pipelines_testdata_base_path + 'reference/GRCh38/vcfanno_functions.lua'
+
+    svdb_query_dbs      = params.pipelines_testdata_base_path + 'reference/GRCh38/svdb_querydb_files.csv'
+
+    genmod_score_config_snv = params.pipelines_testdata_base_path + 'reference/genmod_score_config_snv.ini'
+    genmod_score_config_sv  = params.pipelines_testdata_base_path + 'reference/genmod_score_config_sv.ini'
+
+    extra_args_cadd_annotate       = '--columns Chrom,Pos,Ref,Alt,-,CADD'
+    extra_args_snv_clinical_filter = " --include '(INFO/GNOMADAF_grpmax <= 0.001 || INFO/GNOMADAF_grpmax == \".\")' "
+    extra_args_snv_research_filter = " --include '(INFO/GNOMADAF_grpmax <= 0.001 || INFO/GNOMADAF_grpmax == \".\")' "
+    extra_args_sv_vep              = '--pick --pick_order mane_select,mane_plus_clinical,canonical,appris,tsl,biotype,ccds,rank,length,ensembl,refseq'
+}
+
+
+process {
+
+    withName: '.*:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' {
+        errorStrategy = 'ignore'
+    }
+
+    withName:'.*PROCESS_SNVS:BCFTOOLS_VIEW_RESEARCH' {
+       ext.args = { [
+       "${params.extra_args_snv_research_filter}",
+       "--output-type z",
+       "--write-index=tbi",
+       ].join(' ') }
+    }
+
+    withName: '.*PROCESS_SNVS:ENSEMBLVEP_VEP' {
+        maxForks = 8
+        memory = { 10.GB * task.attempt }
+        cpus = { 2 * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+
+    withName: '.*PROCESS_SVS:ENSEMBLVEP_VEP' {
+        maxForks = 8
+        memory = { 10.GB * task.attempt }
+        cpus = { 2 * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+
+    withName: '.*ANNOTATE_CADD:CADD' {
+        memory = { 30.GB * task.attempt }
+        cpus = { 1 * task.attempt }
+        time = { 1.h * task.attempt }
+    }
+
+    withName: '.*ANNOTATE_CADD:RENAME_CHR_CADD' {
+        memory = { 1.GB * task.attempt }
+        cpus = { 1 * task.attempt }
+        time = { 1.h * task.attempt }
+    }
+
+    withName: '.*ANNOTATE_CADD:ANNOTATE_INDELS' {
+        memory = { 1.GB * task.attempt }
+        cpus = { 1 * task.attempt }
+        time = { 1.h * task.attempt }
+    }
+
+    withName: '.*ANNOTATE_CADD:BCFTOOLS_VIEW' {
+        memory = { 1.GB * task.attempt }
+        cpus = { 1 * task.attempt }
+        time = { 1.h * task.attempt }
+    }
+
+}

conf/test_full.config

@@ -14,11 +14,27 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    // Metadata
+    case_id          = 'test_case_id'
+    sample_id_tumor  = 'test_sample_id_tumor'
+    sample_id_normal = 'test_sample_id_normal'
+    subject_id       = 'subject_a' // matches the subject_id in the samplesheet of the test data of the oncoanalyser pipeline
+    sex              = 'female'
+
+    // Oncoanalyser input parameters
+    oncoanalyser_nextflow_opts = [
+        '-revision 2.2.0-with-purple-tbi-fix',
+        '-profile test_full,docker',
+        '--max_fastq_records 0', // Matches the test_full.config for oncoanalyser
+        ].join(' ')
+    // oncoanalyser_samplesheet   = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/samplesheet/fastq_eval.subject_a.wgts.tndna_trna.minimal.csv'
+    oncoanalyser_mode          = 'wgts'
+    oncoanalyser_genome        = 'GRCh38_hmf'
+
+    // Oncorefiner input parameters
+    oncorefiner_nextflow_opts = [
+        '-revision ac1a8ed33e014d98ae039a1e83294a23ca9bfa61', // Before adding PROCESS_CNVS and LINX input parameters
+        '-profile docker',
+        ].join(' ')
 
-    // Fasta references
-    fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
 }

tests/default_full.nf.test

@@ -0,0 +1,43 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+
+    test("-profile test_full") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['**pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['oncorefiner/oncorefiner_params.yaml'])
+
+            // The oncorefiner params file contains $workDir for NFCORE_ONCOANALYSER, which varies for every run
+            def oncorefiner_params_file_path = "$outputDir/oncorefiner/oncorefiner_params.yaml"
+            def oncorefiner_params_file = file(oncorefiner_params_file_path)
+            def clean_oncorefiner_params_file_content = oncorefiner_params_file.text.replaceAll("$workDir/.*/results", "<oncoanalyser_work_directory>")
+
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/oncoflow_software_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_path,
+                    // All files with stable contents
+                    stable_content,
+                    // Oncoanalyser params file
+                    file("$outputDir/oncoanalyser/oncoanalyser_params.yaml").text.split("\n"),
+                    // Oncorefiner params file without the run $outputDir path
+                    clean_oncorefiner_params_file_content.split("\n")
+                ).match() }
+            )
+        }
+    }
+}